scripts/notebooks/installing.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "0b0acc08-6ce4-4c7a-abec-966e5abdf370",
   "metadata": {},
   "source": [
    "# **NEMO**\n",
    "\n",
    "\n",
    "In a clean directory we will install NEMO, with the PGPLOT graphics device driver. We will create and integrate a Plummer sphere, and manually compile a NEMO program.\n",
    "\n",
    "This first cell will re-install a clean version of the source code, from github. Since the code is open source, you will not need an account on github, but the **git** command needs to be present on your system.\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "1321a220-12cc-4bf1-99d4-deb454c2c239",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Cloning into 'demo'...\n",
      "remote: Enumerating objects: 85791, done.\u001b[K\n",
      "remote: Counting objects: 100% (2170/2170), done.\u001b[K\n",
      "remote: Compressing objects: 100% (119/119), done.\u001b[K\n",
      "remote: Total 85791 (delta 2110), reused 2091 (delta 2051), pack-reused 83621 (from 4)\u001b[K\n",
      "Receiving objects: 100% (85791/85791), 48.59 MiB | 8.67 MiB/s, done.\n",
      "Resolving deltas: 100% (61507/61507), done.\n"
     ]
    }
   ],
   "source": [
    "cd $HOME\n",
    "mkdir -p NEMO\n",
    "cd NEMO\n",
    "rm -rf demo\n",
    "git clone https://github.com/teuben/nemo demo"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "62e2bfbd-82ca-446c-82e9-3d4801206327",
   "metadata": {},
   "source": [
    "The next cell can always be revisited to redo a configure and build. But we show the version of NEMO just to make sure we are in the right directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "0adaa63d-4a52-4984-86c3-e0319f59cd11",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "12318\n",
      "4.5.1\n"
     ]
    }
   ],
   "source": [
    "cd $HOME/NEMO/demo\n",
    "git rev-list --count HEAD\n",
    "cat VERSION"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8eeb144a-fc34-4769-9b32-c5640fa6d956",
   "metadata": {},
   "source": [
    "Now we can configure the package.  We need to configure with a YAPP graphics driver.  YAPP stands for *Yet Another Plotting Package*.  If \"pgplot\" does not work, pick the \"ps\" (postscript) driver.   There is also an \"svg\" in development which might be more fun to display actual results, though in practice the PGPLOT\n",
    "driver is normally used."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "aee511ff-a61e-4497-8111-e5ab2ea18bcd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "checking NEMO config... checking build system type... x86_64-unknown-linux-gnu\n",
      "checking host system type... x86_64-unknown-linux-gnu\n",
      "Found CANONICAL_HOST = linux-gnu or x86_64-unknown-linux-gnu or x86_64\n",
      "Found CANONICAL_BUILD = x86_64-unknown-linux-gnu\n",
      "checking target system type... x86_64-unknown-linux-gnu\n",
      "Found CANONICAL_TARGET = x86_64-unknown-linux-gnu\n",
      "checking for gcc... gcc\n",
      "checking whether the C compiler works... yes\n",
      "checking for C compiler default output file name... a.out\n",
      "checking for suffix of executables... \n",
      "checking whether we are cross compiling... no\n",
      "checking for suffix of object files... o\n",
      "checking whether the compiler supports GNU C... yes\n",
      "checking whether gcc accepts -g... yes\n",
      "checking for gcc option to enable C11 features... none needed\n",
      "checking for stdio.h... yes\n",
      "checking for stdlib.h... yes\n",
      "checking for string.h... yes\n",
      "checking for inttypes.h... yes\n",
      "checking for stdint.h... yes\n",
      "checking for strings.h... yes\n",
      "checking for sys/stat.h... yes\n",
      "checking for sys/types.h... yes\n",
      "checking for unistd.h... yes\n",
      "checking for sys/time.h... yes\n",
      "checking for sys/param.h... yes\n",
      "checking for vfork.h... no\n",
      "checking size of float... 4\n",
      "checking size of double... 8\n",
      "checking size of long double... 16\n",
      "checking size of char... 1\n",
      "checking size of short... 2\n",
      "checking size of int... 4\n",
      "checking size of long... 8\n",
      "checking size of long long... 8\n",
      "checking for grep that handles long lines and -e... /usr/bin/grep\n",
      "checking for egrep... /usr/bin/grep -E\n",
      "checking for strchr... yes\n",
      "checking for memcpy... yes\n",
      "checking for vendor's cc to be used instead of gcc... checking for cc... gcc\n",
      "checking whether the compiler supports GNU C... (cached) yes\n",
      "checking whether gcc accepts -g... (cached) yes\n",
      "checking for gcc option to enable C11 features... (cached) none needed\n",
      "checking for g++... g++\n",
      "checking whether the compiler supports GNU C++... yes\n",
      "checking whether g++ accepts -g... yes\n",
      "checking for g++ option to enable C++11 features... none needed\n",
      "checking for gawk... gawk\n",
      "checking for a BSD-compatible install... /usr/bin/install -c\n",
      "checking whether ln -s works... yes\n",
      "checking whether make sets $(MAKE)... yes\n",
      "checking for ranlib... ranlib\n",
      "checking for the (t)csh shell yes... yes\n",
      "checking for gmake... gmake\n",
      "checking whether gmake is GNU Make... yes\n",
      "checking which precision NEMO is going to use... \n",
      "checking if the gnu coverage tool is to be used... no\n",
      "LFS selected, note that some filesystems may not support Large File anyways\n",
      "Test this with the NEMO command:\n",
      "     mkspiral s000 1000000 nmodel=40\n",
      "checking how to run the C preprocessor... gcc -E\n",
      "checking for X... libraries , headers \n",
      "checking for gethostbyname... yes\n",
      "checking for connect... yes\n",
      "checking for remove... yes\n",
      "checking for shmat... yes\n",
      "checking for IceConnectionNumber in -lICE... yes\n",
      "checking for glBegin in -lGL... yes\n",
      "checking for gluProject in -lGLU... no\n",
      "checking for glBegin in -lMesaGL... no\n",
      "couldn't find OpenGL libraries!\n",
      "checking for bgnqstrip in -lgl_s... no\n",
      "****************************************************\n",
      "You need to install a 3D graphics library, preferably\n",
      "the free OpenGL replacement, Mesa.  You can download\n",
      "Mesa from the Mesa home page:\n",
      "              http://www.mesa3d.org/\n",
      "and install it by running:\n",
      "       ./configure && make && su -c 'make install'\n",
      "in the Mesa directory.\n",
      "You may also need to run /sbin/ldconfig as root\n",
      "to update the system after installing Mesa.\n",
      "(First, add '/usr/local/lib' to /etc/ld.so.conf if\n",
      "you installed Mesa under /usr/local, the default.)\n",
      "****************************************************\n",
      "checking for XMesaGetBackBuffer... no\n",
      "checking whether we have a FORTRAN 77 compiler... checking for gfortran... gfortran\n",
      "checking whether the compiler supports GNU Fortran 77... yes\n",
      "checking whether gfortran accepts -g... yes\n",
      "checking how to get verbose linking output from gfortran... -v\n",
      "checking for Fortran 77 libraries of gfortran...  -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath\n",
      "checking how f77 mangles function names... lowercase-underscore\n",
      "checking if f77 functions with an underscore get an extra underscore... no\n",
      "checking for f77 flags to use C main function... none\n",
      "configure: WARNING: f77 cmain ok\n",
      "checking size of unformatted fortran I/O header/footer... 4\n",
      "checking what flags we need to created shared libs... -fpic\n",
      "checking whether we have PGPLOT... yes, found $PGPLOT_DIR=/usr/lib/pgplot5\n",
      "yes, /usr/lib/pgplot5\n",
      "no\n",
      "checking for PLPlot pkg-config info... no\n",
      "checking for plplot.h... no\n",
      "checking for plplot/plplot.h... no\n",
      "checking for c_plinit in -lplplotd... no\n",
      "configure: WARNING: PLPlot library not found/incomplete! Plotting deactivated.\n",
      "Trying to find LOADOBJ options for linux-gnu ; host=x86_64-unknown-linux-gnu\n",
      "checking for sqrt in -lm... yes\n",
      "checking whether we have HDF4... no\n",
      "configure: WARNING: could not find HDF library\n",
      "configure: WARNING: CFITSIO disabled\n",
      "checking whether we have MIRIAD... no\n",
      "configure: WARNING: could not find MIRIAD library...\n",
      "configure: WARNING: TCL disabled\n",
      "checking for tputs in -lncurses... yes\n",
      "checking for readline/history.h... yes\n",
      "checking for append_history in -lhistory... yes\n",
      "checking for readline/readline.h... yes\n",
      "checking for readline in -lreadline... yes\n",
      "checking for DFSDndataset in -ldf... no\n",
      "checking for foreground in -lvogl... no\n",
      "checking for inflate in -lz... yes\n",
      "checking for strtoll in -lc... yes\n",
      "checking for strtoull in -lc... yes\n",
      "checking for dlopen in -ldl... yes\n",
      "checking for shl_load in -ldld... no\n",
      "checking for library containing dlopen... none required\n",
      "checking for library containing sin... -lm\n",
      "checking for library containing cblas_daxpy... -lgslcblas\n",
      "checking for library containing gsl_version... -lgsl\n",
      "checking for dirent.h that defines DIR... yes\n",
      "checking for library containing opendir... none required\n",
      "checking for egrep... (cached) /usr/bin/grep -E\n",
      "checking for sys/wait.h that is POSIX.1 compatible... yes\n",
      "checking for fcntl.h... yes\n",
      "checking for limits.h... yes\n",
      "checking for malloc.h... yes\n",
      "checking for sgtty.h... yes\n",
      "checking for strings.h... (cached) yes\n",
      "checking for sys/file.h... yes\n",
      "checking for sys/ioctl.h... yes\n",
      "checking for sys/time.h... (cached) yes\n",
      "checking for unistd.h... (cached) yes\n",
      "checking for an ANSI C-conforming const... yes\n",
      "checking for inline... inline\n",
      "checking for off_t... yes\n",
      "checking for size_t... yes\n",
      "checking whether struct tm is in sys/time.h or time.h... time.h\n",
      "checking for long file names... yes\n",
      "checking for special C compiler options needed for large files... no\n",
      "checking for _FILE_OFFSET_BITS value needed for large files... no\n",
      "checking for uid_t in sys/types.h... yes\n",
      "checking type of array argument to getgroups... gid_t\n",
      "checking whether gcc needs -traditional... no\n",
      "checking for working memcmp... yes\n",
      "checking for getpagesize... yes\n",
      "checking for fork... yes\n",
      "checking for vfork... yes\n",
      "checking for vprintf... yes\n",
      "checking for working mmap... yes\n",
      "checking return type of signal handlers... void\n",
      "checking for pid_t... yes\n",
      "checking for working fork... yes\n",
      "checking for working vfork... (cached) yes\n",
      "checking for ftime... yes\n",
      "checking for gethostname... yes\n",
      "checking for gettimeofday... yes\n",
      "checking for getwd... yes\n",
      "checking for mkdir... yes\n",
      "checking for select... yes\n",
      "checking for strdup... yes\n",
      "checking for strtod... yes\n",
      "checking for strtol... yes\n",
      "checking for strtoul... yes\n",
      "checking for dprintf... yes\n",
      "checking for log2... yes\n",
      "checking whether byte ordering is bigendian... no\n",
      "Using NEMOTARS=/home/teuben/NEMO/tar\n",
      "checking looking for a reasonable YAPP... configure: WARNING: using\n",
      "pgplot\n",
      "configure: WARNING: not using opt\n",
      "*** Warning: NEMO=/home/teuben/NEMO/demo, maybe you are running NEMO already\n",
      "configure: creating ./config.status\n",
      "config.status: creating Makefile\n",
      "config.status: creating makedefs\n",
      "config.status: creating nemo-config\n",
      "config.status: creating nemo_start.csh\n",
      "config.status: creating nemo_start.sh\n",
      "config.status: creating nemo_start.py\n",
      "config.status: creating usr/dehnen/utils/make.sh\n",
      "config.status: creating config.h\n",
      "\n",
      "-------------------------------------------------------------------------\n",
      "All done configuring, continue with your installation with\n",
      "\n",
      "     make build check bench5\n",
      "\n",
      "Users need to source the nemo_start.(c)sh file in their shell to\n",
      "enable NEMO commands and set up their NEMO environment.\n",
      "If there any compile or linkings problems, check out $NEMOLIB/makedefs\n",
      "-------------------------------------------------------------------------\n",
      "\n"
     ]
    }
   ],
   "source": [
    "date0=$(date)\n",
    "\n",
    "./configure --with-yapp=pgplot\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9c9c1adf-434c-4a93-a924-a124668c8d5a",
   "metadata": {},
   "source": [
    "The next step is building the software (libraries and binaries) in place. NEMO does normally not install itself in some /usr/local/bin type directory, the build is done in-place. This has some impact how users can use NEMO. More about that later.\n",
    "\n",
    "The **make build** will do a basic install:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "073e0ba5-a522-4544-95d3-d20fbd455d38",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh ; make postconfig mknemos)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo'\n",
      "Checking directory structure on Mon Jan 20 03:32:42 PM EST 2025\n",
      "By teuben on pop-os\n",
      "No tar symlink\n",
      "Updating /home/teuben/NEMO/demo/adm/TIMESTAMP file on Mon Jan 20 03:32:42 PM EST 2025\n",
      "Creating /home/teuben/NEMO/demo/etc/motd file on Mon Jan 20 03:32:42 PM EST 2025\n",
      "Creating /home/teuben/NEMO/demo/nemo_local.csh file on Mon Jan 20 03:32:42 PM EST 2025\n",
      "Creating /home/teuben/NEMO/demo/nemo_local.sh file on Mon Jan 20 03:32:42 PM EST 2025\n",
      "Done with dirs at Mon Jan 20 03:32:42 PM EST 2025\n",
      "cp config.h makedefs /home/teuben/NEMO/demo/lib\n",
      "Installing scripts on Mon Jan 20 03:32:42 PM EST 2025\n",
      "By teuben on pop-os\n",
      "(cd /home/teuben/NEMO/demo/src/scripts; make install)\n",
      "make[2]: Entering directory '/home/teuben/NEMO/demo/src/scripts'\n",
      "cp Makefile.lib /home/teuben/NEMO/demo/lib\n",
      "cp mknemo mkpdoc manlaser nemoman nemobench ldso nemo.version fitsedit fitsmerge nds9 shtool nemo.coverage showvar mir2nemo getline pedit wgetc yapp_query nemoplot nemopars nemo sbatch_nemo.sh nemo_functions.sh progress_bar.sh python/tabplot.py python/fitsplot.py python/mkrunfile.py /home/teuben/NEMO/demo/bin\n",
      "utilities installed\n",
      "make[2]: Leaving directory '/home/teuben/NEMO/demo/src/scripts'\n",
      "MKNEMOS=\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo'\n",
      "Continue with \"make build2 (or build2a build2b)\"\n",
      "(source nemo_start.sh ; make scripts libs)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo'\n",
      "Installing scripts on Mon Jan 20 03:32:42 PM EST 2025\n",
      "By teuben on pop-os\n",
      "(cd /home/teuben/NEMO/demo/src/scripts; make install)\n",
      "make[2]: Entering directory '/home/teuben/NEMO/demo/src/scripts'\n",
      "cp Makefile.lib /home/teuben/NEMO/demo/lib\n",
      "cp mknemo mkpdoc manlaser nemoman nemobench ldso nemo.version fitsedit fitsmerge nds9 shtool nemo.coverage showvar mir2nemo getline pedit wgetc yapp_query nemoplot nemopars nemo sbatch_nemo.sh nemo_functions.sh progress_bar.sh python/tabplot.py python/fitsplot.py python/mkrunfile.py /home/teuben/NEMO/demo/bin\n",
      "utilities installed\n",
      "make[2]: Leaving directory '/home/teuben/NEMO/demo/src/scripts'\n",
      "Starting at Mon Jan 20 03:32:42 PM EST 2025, tail -f /home/teuben/NEMO/demo/install.log\n",
      "(cd src/tutor/main; rm -f maine.o; make -f /home/teuben/NEMO/demo/lib/makedefs  maine.o CFLAGS=\"-v -c\")  >> install.log 2>&1 \n",
      "(cd src;make -i -j  clean install) >> install.log 2>&1\n",
      "(cd usr/dehnen; make -i clean all) >> install.log 2>&1 \n",
      "Done at Mon Jan 20 03:33:54 PM EST 2025\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo'\n",
      "Continue with \"make build3\"\n",
      "(source nemo_start.sh ; make -j  bins)\n",
      "make[1]: Entering directory '/home/teuben/NEMO/demo'\n",
      "Starting at Mon Jan 20 03:33:54 PM EST 2025, tail -f /home/teuben/NEMO/demo/install.log\n",
      "cd src;make -i -j  bins >> ../install.log 2>&1 \n",
      "cd usr;make -i -j  bins >> ../install.log 2>&1 \n",
      "Done at Mon Jan 20 03:34:06 PM EST 2025\n",
      "make[1]: Leaving directory '/home/teuben/NEMO/demo'\n",
      "Continue with \"make build4 for advanced runs\"\n",
      " and/or \"make check bench5\" for a final check\n"
     ]
    }
   ],
   "source": [
    "make build"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e92c25b4-4cb5-45da-bde8-4da5ff537a7a",
   "metadata": {},
   "source": [
    "Check if the build was ok. A number of tests produce a data file which is regressed against a known answer. If these fail, you would see lines starting with **BSF** on the screen. \n",
    "\n",
    "The **make check** will do this:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "6aaa76a2-df8d-4993-86be-7f34d252cba3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh; src/scripts/testsuite | tee -a install.log )\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/fits\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/rotcur\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/trans\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/image/wcs\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/kernel/fortran\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/kernel/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/kernel/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/kernel/tab\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/cores\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/aarseth/nbody0\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/aarseth/tools\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/dehnen\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/directcode\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/flowcode\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/hackcode/hackcode1\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/hackcode/treecode1\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/scfm\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/evolve/sellwood/tools\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/image\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/init\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/io_nemo\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/io/starlab\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/io\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/reduc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/trans\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/nbody/xyz\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/orbit/misc\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/src/orbit/potential\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/usr/hannorein\n",
      "TESTSUITE: OK   /home/teuben/NEMO/demo/usr/wolfire\n",
      "Results in /home/teuben/NEMO/demo/tmp/test762381/testsuite.log\n",
      "A copy in /home/teuben/NEMO/demo/testsuite.log is kept as well as the latest.\n",
      "BSF regressions that are OK: 64\n",
      "There are 300 binaries in NEMO\n",
      "TESTSUITE started Mon Jan 20 03:34:06 PM EST 2025\n",
      "TESTSUITE   ended Mon Jan 20 03:34:14 PM EST 2025\n"
     ]
    }
   ],
   "source": [
    "make check\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5fabc543-1178-46b5-8e34-0c7fca002e0b",
   "metadata": {},
   "source": [
    "And finally a benchmark to check how the speed compares with an otherwise random 2020-type laptop. Currently 6 nbody codes are run, each of them typically taking 5 seconds to compute.\n",
    "\n",
    "The **make bench5** will do this:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "0f432f58-e93a-4469-8754-83474b0d0e2d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(source nemo_start.sh; /usr/bin/time src/scripts/nemo.bench mode=5 | tee -a install.log )\n",
      "NEMOBENCH: (2024-10-18) bench764077 : nbody0=3072 nbody1=10240 nbody3=1000000 size=256 ften=1 clean=1 bsf=0 tmp=bench764077\n",
      "pop-os\n",
      "Linux pop-os 6.9.3-76060903-generic #202405300957~1726766035~22.04~4092a0e SMP PREEMPT_DYNAMIC Thu S x86_64 x86_64 x86_64 GNU/Linux\n",
      "Mon Jan 20 03:34:15 PM EST 2025\n",
      "Equal 5sec CPU time per code, no output files to check\n",
      "Codes:  directcode [mkplummer] gyrfalcON hackcode1 [mkorbit] orbint potcode treecode1\n",
      "Tstop: 4.28*1 5.64*1 7.89*1 787400.0*1 6.66*1 3.00*1 [5sec CPU for each on a 11th Gen Intel(R) Core(TM) i5-1135G7 up to 4.2GHz using gcc-11]\n",
      ".1.23.456.\n",
      "CPU_USAGE  directcode  :  4.72  4.71  0.00  0.00  0.00  721841408\n",
      "CPU_USAGE  gyrfalcON   :  3.63  3.63  0.00  0.00  0.00  721841882\n",
      "CPU_USAGE  hackcode1   :  4.05  4.04  0.00  0.00  0.00  721842246\n",
      "CPU_USAGE  orbint      :  3.65  3.64  0.00  0.00  0.00  721842652\n",
      "CPU_USAGE  potcode     :  3.67  3.66  0.00  0.00  0.00  721843018\n",
      "CPU_USAGE  treecode1   :  4.35  4.34  0.00  0.00  0.00  721843386\n",
      "NEMOBENCH5 score:   1246.36\n",
      "Cleaning bench764077 (use clean=0 to prevent this)\n",
      "24.08user 0.08system 0:24.17elapsed 99%CPU (0avgtext+0avgdata 7892maxresident)k\n",
      "0inputs+4104outputs (0major+9591minor)pagefaults 0swaps\n"
     ]
    }
   ],
   "source": [
    "make bench5\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c8e86ee9-12ef-408e-a332-d9e97801fce9",
   "metadata": {},
   "source": [
    "Any score over 1000 is pretty good."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f404780a-63ef-49bb-ba4a-4a4285cf9a1b",
   "metadata": {},
   "source": [
    "# Using NEMO\n",
    "Now the package is ready for anybody to use. For this a user needs to source the **nemo_start.sh** file in their shell before NEMO commands are available. \n",
    "\n",
    "In our case here:\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "927ef176-acf8-4fba-b32d-838436d75ebc",
   "metadata": {},
   "outputs": [],
   "source": [
    "source $HOME/NEMO/demo/nemo_start.sh"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c15a7fbf-ad3c-4b5e-ab40-34dc2abacf63",
   "metadata": {},
   "source": [
    "and now the **nemo** command is available to check your active version of NEMO, and some other important\n",
    "variables."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "8ab13683-e91b-44be-a516-99a1e8183069",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NEMO:        /home/teuben/NEMO/demo  - Version:4.5.1\n",
      "YAPP:        /xs - default yapp plotting device\n",
      "git:         Branch:master     Counter:12318      Date: 2025/01/20_10:43:06\n",
      "python:      /home/teuben/NEMO/nemo/anaconda3/bin/python  - Python 3.12.4\n",
      "OS_release:  Linux Description:\tPop!_OS 22.04 LTS\n"
     ]
    }
   ],
   "source": [
    "nemo"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dc2b4aeb-4352-41bb-a353-9f66e3de5808",
   "metadata": {},
   "source": [
    "## A Plummer sphere\n",
    "\n",
    "To create a Plummer (1911) sphere with 128 particles the **mkplummer** program can be used.\n",
    "\n",
    "First a few ways to get help on this program\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "02a07713-7ecc-421e-a6ee-514d6125c100",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "out              : Output file name [???]\n",
      "nbody            : Number of particles [???]\n",
      "mlow             : Low mass fraction cutoff of Plummer dist [0]\n",
      "mfrac            : Mass fraction used of Plummer distribution [0.999]\n",
      "rfrac            : Radius fraction used of Plummer distribution\n",
      "                              NOTE: the above two values are chosen so\n",
      "                                    that m( rfrac ) = mfrac                 [22.8042468]\n",
      "seed             : Seed for the random number generator [0]\n",
      "time             : Time at which snapshot is taken [0.0]\n",
      "zerocm           : Centrate snapshot (t/f)? [t]\n",
      "scale            : Model scale factor (-1=virial 1=natural) [-1]\n",
      "quiet            : 0=noisy 1=somewhat quiet 2=more quiet [0]\n",
      "massname         : If used Mass-function name (e.g. n(m)) []\n",
      "massexpr         : Mass function expression (e.g. pow(m,p)) [pow(m,p)]\n",
      "masspars         : Mass function parameters (e.g. p,0.0) [p,0.0]\n",
      "massrange        : Range for mass-spectrum (e.g. 1,2) [1,1]\n",
      "headline         : Verbiage for output []\n",
      "nmodel           : number of models to produce [1]\n",
      "mode             : 0=no data,  1=data, no analysis 2=data, analysis [1]\n",
      "VERSION          : 6-jun-2024 PJT [3.0c]\n"
     ]
    }
   ],
   "source": [
    "mkplummer help=h"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b62a119d-3c32-4d69-8ea6-cbbb583b4680",
   "metadata": {},
   "source": [
    "Although the **man** command can be used to get the manual page displayed, NEMO programs also accept the **--man** argument to achieve the same thing:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "7f205416-6dda-4f05-b63a-0a0cbb12bffb",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKPLUMMER(1NEMO)                                              MKPLUMMER(1NEMO)\n",
      "\n",
      "NAME\n",
      "       mkplummer - construct a Plummer model\n",
      "\n",
      "SYNOPSIS\n",
      "       mkplummer [parameters=values...]\n",
      "\n",
      "DESCRIPTION\n",
      "       mkplummer  constructs  an N-body realization of a Plummer model, with a\n",
      "       spatial or mass based cut-off, after which it (optionally)  performs  a\n",
      "       coordinate  transformation to the center-of-mass coordinate system. The\n",
      "       data are then written into a file snap-file, in a standard N-body snap‐\n",
      "       shot(5NEMO)  format.  The model is constructed in VIRIAL or NBODY units\n",
      "       (M=G=-4E=1, with E the total energy), and finite spatial  extent  which\n",
      "       can  be  regulated  by specifying mfrac or rfrac or using their default\n",
      "       values.  The distribution function of a Plummer  model  is  spherically\n",
      "       symmetric  and  isotropic, and is a polytrope of index n = 5.  See also\n",
      "       Aarseth et al. (1974) and Plummer (1911).\n",
      "\n",
      "       There is also an implementation in Dehnen's falcON suite:  mkplum(1fal‐\n",
      "       cON)\n",
      "\n",
      "       For more advanced Plummer models, see mcluster(1NEMO).\n",
      "\n",
      "PARAMETERS\n",
      "       The  following parameters are recognized in order; they may be given in\n",
      "       any order if the keyword is also given. Use --help to confirm this  man\n",
      "       page is up to date.\n",
      "\n",
      "       out=snapfile             Output data is written into snapfile, in stan‐\n",
      "                                dard snapshot(5NEMO) format.\n",
      "                                No default\n",
      "\n",
      "       nbody=integer            Number of particles in the model.\n",
      "                                No default.\n",
      "\n",
      "       mlow=real                inner core mass fraction within which no stars\n",
      "                                will be populated.\n",
      "                                [Default: 0]\n",
      "\n",
      "       mfrac=real               mass fraction of the (otherwise infinitely ex‐\n",
      "                                tended) Plummer model; see  rfrac  immediately\n",
      "                                below  Note  that the total mass is still nor‐\n",
      "                                malized to 1.\n",
      "                                [Default: rfrac=22.8042468]\n",
      "\n",
      "       rfrac=real               radius fraction of the  (otherwise  infinitely\n",
      "                                extended)  Plummer  model. If mfrac = 1.0 then\n",
      "                                particles will be sprinkled in all over space.\n",
      "                                If mfrac < 1.0 or rfrac > 0.0 then each parti‐\n",
      "                                cle is constrained to lie within both the  ra‐\n",
      "                                dial  and  (cumulative) mass bound.  For exam‐\n",
      "                                ple, if rfrac( mfrac ) > rfrac then  rfrac  is\n",
      "                                the  limiting  factor, but if rfrac( mfrac ) <\n",
      "                                rfrac then mfrac  limits  the  extent  of  the\n",
      "                                Plummer  realization.  Note: specifying either\n",
      "                                value may have no effect if the default  value\n",
      "                                of  the  other parameter is still the limiting\n",
      "                                factor;   Beware!    (Default:    mfrac=0.999;\n",
      "                                rfrac=22.8042468  , chosen so that the cumula‐\n",
      "                                tive mass at rfrac is mfrac).\n",
      "                                Default: ....\n",
      "\n",
      "       seed=integer             seed for the random number generator. A  value\n",
      "                                of  0  (the  default) will be converted into a\n",
      "                                unique new value using UNIX's clock  time,  in\n",
      "                                seconds since 1970.0). See also xrandom(1NEMO)\n",
      "                                for more options.\n",
      "                                [Default: 0]\n",
      "\n",
      "       time=time                Time at which the snapshot applies\n",
      "                                [Default: 0.0]\n",
      "\n",
      "       zerocm=t|f               Reset center of mass to zero?\n",
      "                                [Default: t].\n",
      "\n",
      "       scale=scale_factor       A  scale  factor  or  scale  to  virial  units\n",
      "                                (M=G=-4E=1). Use -1 for virial units (see also\n",
      "                                UNITS below), and 1 to get a model  in  struc‐\n",
      "                                tural (natural) units.  Note: large scale fac‐\n",
      "                                tors means small systems with  large  velocity\n",
      "                                disperson.\n",
      "                                [Default: -1].\n",
      "\n",
      "       quiet=level              Level  of  quit  start. 0 is noisy, 1=somewhat\n",
      "                                quiet, 2=more quiet. See \"QUIET START\" below\n",
      "                                [Default: 0].\n",
      "\n",
      "       massname=name            Identification of the  mass  spectrum.  It  is\n",
      "                                normally only a function of mass, so n(m) will\n",
      "                                suffice. If nothing specified, all stars  will\n",
      "                                have the same mass (total mass M=1).\n",
      "                                [Default: not used].\n",
      "\n",
      "       massexpr=expr            Expression  for the mass-spectrum. In addition\n",
      "                                to the mass m from the massname it may contain\n",
      "                                any  variables contained in the masspars to be\n",
      "                                specified next.\n",
      "                                [Default: pow(m,p)].\n",
      "\n",
      "       masspars=pars            List of parameters and their values. They  can\n",
      "                                be  used by name in the massexpr specified be‐\n",
      "                                fore.\n",
      "                                [Default: p,0.0].\n",
      "\n",
      "       massrange=mlow,mhigh     Valid massrange. A  lower  and  higher  cutoff\n",
      "                                must  be supplied. The massrange has arbitrary\n",
      "                                units, since all masses will  be  rescaled  to\n",
      "                                set the total mass M=1.\n",
      "                                [Default: 1,1].\n",
      "\n",
      "       headline=string          Optional  headline,  which  is  written as the\n",
      "                                first item in the snapshot file, the next item\n",
      "                                being the snapshot itself.\n",
      "                                [Default: not used].\n",
      "\n",
      "       nmodel=integer           Number  of models to generate. Although mostly\n",
      "                                meant for benchmarks, generating more  then  1\n",
      "                                model  can  be  useful  to  process very large\n",
      "                                snapshots (that normally won't fit in  memory)\n",
      "                                in  a  serialized fashion. See also snapsplit.\n",
      "                                Most NEMO programs will only  read  the  first\n",
      "                                snapshot.\n",
      "                                [Default: 1]\n",
      "\n",
      "       mode=0|1|2               The  processing  mode,  purely  for  debugging\n",
      "                                benchmarks.  0=no data written.  1=data  writ‐\n",
      "                                ten,  but  no extra analysis.  2=data written,\n",
      "                                and extra analysis done.\n",
      "                                [Default: 1]\n",
      "\n",
      "UNITS\n",
      "       The scale length of a Plummer sphere  in  virial  units  is  3.pi/16  ~\n",
      "       0.589.   As  an example the following two commands should plot the same\n",
      "       \"rotation\" curve:\n",
      "\n",
      "        mkplummer - 10000 | radprof - tab=t | tabplot - 1 3 0 2 0 1 yapp=1/xs\n",
      "        rotcurves plummer '0,1,3*pi/16' xrange=0,2 yrange=0,1       yapp=2/xs\n",
      "\n",
      "QUIET START\n",
      "       For small N-body systems it can easily happen that small random fluctu‐\n",
      "       ations  cause  a  unacceptabel  large  deviation  from an ideal Plummer\n",
      "       sphere. One way to achieve more \"quiet\" initial conditions is by  posi‐\n",
      "       tioning  the  particles  more \"uniformly\" in their 1/N mass shells, in‐\n",
      "       stead of uniformly filling the space between 0  and  1.  This  is  con‐\n",
      "       trolled  by  the  quiet=1  setting.    An  even more quiet start can be\n",
      "       achieved by placing the particles on exactly the radius compatible with\n",
      "       its mass fraction, this is achieved with the the quiet=2 setting.\n",
      "\n",
      "       In  this  example  you can clearly see the difference between the radii\n",
      "       selected:\n",
      "\n",
      "        mkplummer - 10 quiet=0 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "        mkplummer - 10 quiet=1 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "        mkplummer - 10 quiet=2 zerocm=f | snapsort - - r | snapprint - r | tabplot - 0 1 line=1,1 point=2,0.1\n",
      "\n",
      "       Important to note that with zerocm=f the center  of  mass  will  drift,\n",
      "       while  the  \"mathematical  center\"  was placed at the origin. This will\n",
      "       counter the quietness, if you will.\n",
      "\n",
      "CAVEATS\n",
      "       A non-delta function mass-spectrum will not create a  properly  virial‐\n",
      "       ized system yet. See snapvirial(1NEMO)\n",
      "\n",
      "       For  very  large (>1000) ratio in the mass ranges the spline interpola‐\n",
      "       tion, used in frandom(3NEMO), can fail using a valid [0,1] range.\n",
      "\n",
      "EXAMPLES\n",
      "       mkplummer can also be used to create a plummer sphere with a mass spec‐\n",
      "       trum, e.g.  a Salpeter mass spectrum with\n",
      "\n",
      "        mkplummer salpeter.dat 10000 massname='n(m)' massexpr='pow(m,p)' masspars=p,-2.35 massrange=0.1,10\n",
      "\n",
      "       Another  method to create a Plummer sphere is by using the Osipkov-Mer‐\n",
      "       ritt tables in NEMO, e.g.\n",
      "\n",
      "        plummer plum.dat ntab=1024\n",
      "        mkommod plum.dat plum.snap nbody=10000\n",
      "\n",
      "       or in ZENO their new General Spherical Profile:\n",
      "\n",
      "        plumsnap plum1.snap\n",
      "\n",
      "        plumgsp plum.gsp\n",
      "        gsprealize plum.gsp plum.snap zerocm=true\n",
      "        snapcopy plum.snap plum2.snap\n",
      "\n",
      "       with a note that ZENO files may need an  extra  snapcopy(1NEMO)  to  be\n",
      "       compatible with NEMO snapshot(5NEMO) files.\n",
      "\n",
      "BENCHMARKS\n",
      "       The  default benchmark (see Benchfile) creates a 10,000,000 snapshot in\n",
      "       double precision, with and without writing to a local file:\n",
      "\n",
      "        cd $NEMO/nemo/src/nbody/init/\n",
      "        make -f Benchfile bench0 bench1\n",
      "\n",
      "           or\n",
      "\n",
      "        /usr/bin/time mkplummer . 10000000\n",
      "        /usr/bin/time mkplummer bench1.snap 10000000\n",
      "\n",
      "       with some sample CPU for bench0:\n",
      "          xps13       3.1s  or 171 MB/s\n",
      "          t480        4.9s  or  72 MB/s\n",
      "       the time difference betweeen bench0 and bench1 can  be  interpreted  as\n",
      "       the time needed to write 535MB (for 10M particles)\n",
      "\n",
      "FILES\n",
      "       NEMO/src/nbody/init/mkplummer.c\n",
      "\n",
      "SEE ALSO\n",
      "       mkpolytrope(1NEMO),    snapvirial(1NEMO),    mkplummer(3NEMO),    snap‐\n",
      "       mass(1NEMO), snapsplit(1NEM0),  mkplum(1NEMO),  mcluster(1NEMO),  xran‐\n",
      "       dom(3NEMO)\n",
      "\n",
      "       H.C.Plummer (1911), MNRAS, 71, 460.\n",
      "\n",
      "       S.J.  Aarseth,  M.  Henon and R.  Wielen (1974), Astron. and Astrophys.\n",
      "       37, p. 183.\n",
      "\n",
      "       A.H.W. Kuepper, Th. Maschberger, P. Kroupa and H. Baumgardt, 2011,  MN‐\n",
      "       RAS, 417, 2300 (McLuster)\n",
      "\n",
      "       Arnold    et    al.   (2022)   -   https://arxiv.org/abs/2207.10681   -\n",
      "       https://github.com/r-j-arnold/gen_fractal_star_clusters\n",
      "\n",
      "ADS\n",
      "       @ads 1974A&A....37..183A\n",
      "\n",
      "AUTHOR\n",
      "       Piet Hut (Peter Teuben)\n",
      "\n",
      "FILES\n",
      "       ~/src/nbody/init              mkplummer.c\n",
      "\n",
      "HISTORY\n",
      "       23-Apr-87   Version 1.0: created                         PIET\n",
      "       10-Jun-88   Version 1.1: created                         PIET\n",
      "       xx-xxx-88   V1.2: zerocm keyword added                   PJT\n",
      "       xx-Mar-89   V2.0: full new snapshot version+doc          PJT\n",
      "       15-nov-90   V2.3: mass-spectrum and cleanup for NEMO 2.x PJT\n",
      "       6-jun-96    V2.5d: report total mass before scaling      PJT\n",
      "       21-mar-04   V2.7: added mlow=                            PJT+NCM\n",
      "       11-apr-05   V2.8: added nmodel=                          PJT\n",
      "       15-sep-10   V2.9: clarified rfrac and allow rfrac<0      PJT\n",
      "       2-dec-2017  documented mcluster                          PJT\n",
      "       29-mar-2021 benchmark                                    PJT\n",
      "       25-sep-2023 describe quiet starts                        PJT\n",
      "       1-apr-2024  experimenting with how to place defaults     PJT\n",
      "\n",
      "                                  27 May 2024                 MKPLUMMER(1NEMO)\n"
     ]
    }
   ],
   "source": [
    "mkplummer --man"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8a1eafc8-d460-42be-8d28-f36848977894",
   "metadata": {},
   "source": [
    "Another frequently used reminder is the **--help** option, giving a shorthand of all keywords and their defaults. Keywords with the **???** value are required to get a value. In this case the first two arguments (out, nbody)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "e3618d9c-39cf-44f4-b226-9ca07537a8f1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mkplummer out=??? nbody=??? mlow=0 mfrac=0.999 rfrac=22.8042468 seed=0 time=0.0 zerocm=t scale=-1 quiet=0 massname= massexpr=pow(m,p) masspars=p,0.0 massrange=1,1 headline= nmodel=1 mode=1 VERSION=3.0c\n"
     ]
    }
   ],
   "source": [
    "mkplummer --help\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4eb58e94-4649-4693-bb26-0444c010780d",
   "metadata": {},
   "source": [
    "## Initial conditions\n",
    "\n",
    "From the output of the **--help** the order of the keyword will matter if the order is kepts according to this list. So giving just two values binds them to the **out=** and **nbody=** resp."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "9caccf67-7ea6-4319-bb0a-71cebd7a7b0e",
   "metadata": {},
   "outputs": [],
   "source": [
    "mkplummer p128 128 seed=123"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0d05dabb-f4f2-42ec-a08c-b00becc4fb00",
   "metadata": {},
   "source": [
    "This this would have been equivalent:\n",
    "```\n",
    "     mkplummer out=p128 nbody=128\n",
    "```\n",
    "\n",
    "\n",
    "\n",
    "The contents of NEMO files is usually binary.  So viewing their contents in a more human friendly way is done with the program **tsf** (*type structured file*)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "3ef8397c-1275-44db-a8b0-b7df102cd755",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "char Headline[28] \"init_xrandom: seed used 123\"\n",
      "char History[41] \"mkplummer p128 128 seed=123 VERSION=3.0c\"\n",
      "set SnapShot\n",
      "  set Parameters\n",
      "    int Nobj 128 \n",
      "    double Time 0.00000 \n",
      "  tes\n",
      "  set Particles\n",
      "    int CoordSystem 66306 \n",
      "    double Mass[128] 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      0.00781250 0.00781250 0.00781250 0.00781250 0.00781250 \n",
      "      . . .\n",
      "    double PhaseSpace[128][2][3] -0.561583 -0.0653953 -0.541420 \n",
      "      -0.106656 -0.119243 0.286915 4.85715 -0.329890 -1.61621 0.388497 \n",
      "      0.207920 0.120547 0.593217 0.235838 -0.0272317 0.0567244 \n",
      "      -0.0189743 -0.391682 0.425112 -0.0570265 -0.102289 -0.769960 \n",
      "      . . .\n",
      "  tes\n",
      "tes\n"
     ]
    }
   ],
   "source": [
    "tsf p128"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "d686bf81-1fd0-46ac-97a5-7de42d78492e",
   "metadata": {},
   "outputs": [],
   "source": [
    "snapplot p128 yapp=installing1.png/png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "60d90da4-95b3-4220-95a0-f3d4d944332a",
   "metadata": {},
   "source": [
    "![alt text](installing1.png \"InitialConditions\")\n",
    "\n",
    "\n",
    "## Integrate it:\n",
    "\n",
    "The **hackcode1** program is the original Barnes and Hut (1985) tree code N-logN algorithm to integrate an N-body system."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "eeef980c-e486-43f5-a181-8d50136e7e33",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "init_xrandom: seed used 123\n",
      "\n",
      "       nbody        freq         eps         tol\n",
      "         128       32.00      0.0500      1.0000\n",
      "\n",
      "\toptions: mass,phase\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.000   -0.2396   -0.4900      6543        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000   -0.0000    0.0000\n",
      "\t        cm vel   -0.0000   -0.0000   -0.0000\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.031   -0.2397   -0.4885      6477        31        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel   -0.0000    0.0000   -0.0000\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.062   -0.2399   -0.4874      6456        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000   -0.0000\n",
      "\t        cm vel    0.0000    0.0000    0.0001\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.094   -0.2403   -0.4864      6489        32        18      0.00\n",
      "\n",
      "\t        cm pos    0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0000    0.0000    0.0001\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.125   -0.2400   -0.4865      6509        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0001    0.0001    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.156   -0.2401   -0.4869      6652        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0002    0.0001    0.0003\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.188   -0.2401   -0.4876      6859        34        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0002    0.0001    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.219   -0.2399   -0.4881      6675        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0002    0.0001    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.250   -0.2399   -0.4880      6692        33        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0002    0.0002    0.0002\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.281   -0.2401   -0.4878      6815        35        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0000\n",
      "\t        cm vel   -0.0002    0.0002    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.312   -0.2403   -0.4873      6867        34        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0001\n",
      "\t        cm vel   -0.0002    0.0002    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.344   -0.2405   -0.4872      6844        33        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0000    0.0001\n",
      "\t        cm vel   -0.0002    0.0003    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.375   -0.2408   -0.4868      6817        33        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0001    0.0001\n",
      "\t        cm vel   -0.0001    0.0003    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.406   -0.2406   -0.4870      6843        32        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0001    0.0003    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.438   -0.2408   -0.4869      6850        32        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0001    0.0003    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.469   -0.2413   -0.4859      6767        32        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0002    0.0004    0.0003\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.500   -0.2406   -0.4853      6841        34        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0003    0.0004    0.0002\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.531   -0.2407   -0.4839      6864        35        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0002    0.0005    0.0000\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.562   -0.2407   -0.4830      6904        36        17      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0002    0.0005   -0.0001\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.594   -0.2406   -0.4826      6881        35        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel   -0.0001    0.0005   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.625   -0.2405   -0.4821      6613        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0001    0.0004   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.656   -0.2401   -0.4814      6661        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0001    0.0003   -0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.688   -0.2403   -0.4795      6660        33        18      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0001    0.0001   -0.0001\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.719   -0.2401   -0.4784      6674        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0002    0.0000   -0.0000\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.750   -0.2398   -0.4777      6701        32        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0002   -0.0001    0.0001\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.781   -0.2401   -0.4767      6541        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0001   -0.0001    0.0002\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.812   -0.2400   -0.4763      6506        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel   -0.0000   -0.0002    0.0003\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.844   -0.2399   -0.4760      6517        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0002    0.0001\n",
      "\t        cm vel    0.0001   -0.0002    0.0004\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.875   -0.2398   -0.4761      6541        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel    0.0002   -0.0003    0.0005\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.906   -0.2405   -0.4753      6395        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel    0.0003   -0.0003    0.0006\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.938   -0.2402   -0.4748      6420        30        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0001\n",
      "\t        cm vel    0.0004   -0.0002    0.0008\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       0.969   -0.2406   -0.4732      6287        28        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0002\n",
      "\t        cm vel    0.0004   -0.0001    0.0009\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.000   -0.2406   -0.4721      6511        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0002\n",
      "\t        cm vel    0.0003   -0.0000    0.0009\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.031   -0.2408   -0.4706      6497        30        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0002\n",
      "\t        cm vel    0.0003    0.0001    0.0009\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.062   -0.2407   -0.4694      6505        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0001    0.0001    0.0003\n",
      "\t        cm vel    0.0003    0.0001    0.0009\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.094   -0.2406   -0.4684      6433        31        19      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0001    0.0003\n",
      "\t        cm vel    0.0003    0.0001    0.0010\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.125   -0.2401   -0.4679      6318        29        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0001    0.0003\n",
      "\t        cm vel    0.0003    0.0001    0.0010\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.156   -0.2400   -0.4668      6223        28        20      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0001    0.0004\n",
      "\t        cm vel    0.0003    0.0002    0.0012\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.188   -0.2396   -0.4660      6195        27        21      0.00\n",
      "\n",
      "\t        cm pos   -0.0000    0.0001    0.0004\n",
      "\t        cm vel    0.0004    0.0003    0.0013\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.219   -0.2397   -0.4650      6235        27        21      0.00\n",
      "\n",
      "\t        cm pos    0.0000    0.0002    0.0004\n",
      "\t        cm vel    0.0005    0.0003    0.0015\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.250   -0.2399   -0.4639      6174        26        21      0.00\n",
      "\n",
      "\t        cm pos    0.0000    0.0002    0.0005\n",
      "\t        cm vel    0.0005    0.0003    0.0017\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.281   -0.2396   -0.4633      6285        28        21      0.00\n",
      "\n",
      "\t        cm pos    0.0000    0.0002    0.0005\n",
      "\t        cm vel    0.0004    0.0003    0.0019\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.312   -0.2396   -0.4621      6188        27        21      0.00\n",
      "\n",
      "\t        cm pos    0.0000    0.0002    0.0006\n",
      "\t        cm vel    0.0004    0.0003    0.0021\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.344   -0.2396   -0.4611      6226        27        21      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0002    0.0007\n",
      "\t        cm vel    0.0004    0.0004    0.0022\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.375   -0.2399   -0.4605      6326        28        20      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0002    0.0007\n",
      "\t        cm vel    0.0005    0.0005    0.0023\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.406   -0.2401   -0.4600      6253        28        20      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0002    0.0008\n",
      "\t        cm vel    0.0006    0.0006    0.0025\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.438   -0.2400   -0.4600      6296        28        20      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0002    0.0009\n",
      "\t        cm vel    0.0006    0.0006    0.0026\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.469   -0.2397   -0.4607      6426        29        20      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0003    0.0010\n",
      "\t        cm vel    0.0006    0.0006    0.0027\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.500   -0.2402   -0.4606      6561        32        18      0.00\n",
      "\n",
      "\t        cm pos    0.0001    0.0003    0.0011\n",
      "\t        cm vel    0.0007    0.0007    0.0027\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.531   -0.2404   -0.4602      6321        28        20      0.00\n",
      "\n",
      "\t        cm pos    0.0002    0.0003    0.0011\n",
      "\t        cm vel    0.0007    0.0007    0.0027\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.562   -0.2409   -0.4590      6434        30        19      0.00\n",
      "\n",
      "\t        cm pos    0.0002    0.0003    0.0012\n",
      "\t        cm vel    0.0006    0.0008    0.0028\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.594   -0.2410   -0.4581      6382        29        19      0.00\n",
      "\n",
      "\t        cm pos    0.0002    0.0004    0.0013\n",
      "\t        cm vel    0.0006    0.0008    0.0028\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.625   -0.2409   -0.4575      6376        29        19      0.00\n",
      "\n",
      "\t        cm pos    0.0002    0.0004    0.0014\n",
      "\t        cm vel    0.0006    0.0008    0.0028\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.656   -0.2407   -0.4575      6458        30        19      0.00\n",
      "\n",
      "\t        cm pos    0.0002    0.0004    0.0015\n",
      "\t        cm vel    0.0005    0.0009    0.0027\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.688   -0.2406   -0.4577      6489        32        18      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0004    0.0016\n",
      "\t        cm vel    0.0005    0.0010    0.0027\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.719   -0.2404   -0.4580      6423        30        19      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0005    0.0017\n",
      "\t        cm vel    0.0005    0.0011    0.0028\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.750   -0.2403   -0.4585      6436        31        18      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0005    0.0018\n",
      "\t        cm vel    0.0004    0.0012    0.0028\n",
      "\n",
      "\tparticle data written\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.781   -0.2401   -0.4595      6437        31        18      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0005    0.0018\n",
      "\t        cm vel    0.0004    0.0012    0.0028\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.812   -0.2398   -0.4610      6360        31        17      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0006    0.0019\n",
      "\t        cm vel    0.0004    0.0011    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.844   -0.2400   -0.4623      6302        31        17      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0006    0.0020\n",
      "\t        cm vel    0.0004    0.0011    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.875   -0.2400   -0.4636      6349        30        18      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0006    0.0021\n",
      "\t        cm vel    0.0004    0.0011    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.906   -0.2401   -0.4648      6339        31        18      0.00\n",
      "\n",
      "\t        cm pos    0.0003    0.0007    0.0022\n",
      "\t        cm vel    0.0005    0.0012    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.938   -0.2398   -0.4660      6334        31        18      0.00\n",
      "\n",
      "\t        cm pos    0.0004    0.0007    0.0023\n",
      "\t        cm vel    0.0006    0.0012    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       1.969   -0.2397   -0.4668      6244        29        19      0.00\n",
      "\n",
      "\t        cm pos    0.0004    0.0008    0.0024\n",
      "\t        cm vel    0.0006    0.0012    0.0029\n",
      "\n",
      "        tnow       T+U       T/U     nttot     nbavg     ncavg   cputime\n",
      "       2.000   -0.2400   -0.4670      6235        29        19      0.00\n",
      "\n",
      "\t        cm pos    0.0004    0.0008    0.0025\n",
      "\t        cm vel    0.0008    0.0012    0.0030\n",
      "\n",
      "\tparticle data written\n"
     ]
    }
   ],
   "source": [
    "hackcode1 p128 p128.out tstop=2 "
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ccecb826-155e-4c1b-9455-e09ac1a40fcc",
   "metadata": {},
   "source": [
    "Display some diagnostics, such as energy and center of mass motion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "6c0ebe67-32c8-40c6-8da1-465175882716",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "### nemo Debug Info: 65 diagnostic frames read\n",
      "Worst fractional energy loss dE/E = (E_t-E_0)/E_0 = 0.00695265 at T = 0.46875\n"
     ]
    }
   ],
   "source": [
    "snapdiagplot p128.out yapp=installing2.png/png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f89cf800-6c29-4cb9-b788-090f8012ce6b",
   "metadata": {},
   "source": [
    "This gives around 1% energy conservation, whichis not too bad, at least for galactic type simulations. For star clusters probably not too great at all.\n",
    "\n",
    "![alt text](installing2.png \"IntegrationDiagnostics\")\n",
    "\n",
    "\n",
    "Now plot in a two by two panel the X-Y projections of the integration at times 0, 1 and 2."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ef31bc23-25db-48f5-ab4b-5d0e90fffa86",
   "metadata": {},
   "outputs": [],
   "source": [
    "snapplot p128.out nxy=2,2 times=0,1,2 yapp=installing3.png/png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "620bd7c0-3842-4bec-8101-083c6be82436",
   "metadata": {},
   "source": [
    "![alt text](installing3.png \"EvolutionPlot\")\n",
    "\n",
    "## Compiling code\n",
    "\n",
    "Although the build has done this, the **mknemo** command will recompile a program. This can be useful if the code needs to be edited for a bug fix and new feature. The **mknemo** command can be issued anywhere, and will show where the file in question lives. It can then easily be edited and recompiled, and added to $NEMOBIN. Except for editing, the **mknemo** command does all of this."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "ff99c466-eb36-4008-a9e3-f4dae78bff41",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKNEMO> Searching tsf.c: \n",
      "found one: /home/teuben/NEMO/demo/src/kernel/io/tsf.c\n",
      "gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -fpic -rdynamic  -Dlinux -DSYSV  -I/home/teuben/NEMO/demo/inc -I/home/teuben/NEMO/demo/lib -I/home/teuben/NEMO/demo/opt/include    -Wall -Wimplicit-function-declaration  -D_GNU_SOURCE -std=c99  -o tsf tsf.c -L/home/teuben/NEMO/demo/lib -L/home/teuben/NEMO/demo/opt/lib          -lnemo -ldl  -lreadline -lhistory -lncurses  -lm   -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath \n",
      "\n"
     ]
    }
   ],
   "source": [
    "mknemo tsf"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "322147e8-4bd9-4eee-b0e3-df2356c56b9b",
   "metadata": {},
   "source": [
    "The output also reminds you wehre the **tsf.c** source code lives, so it can be easily put in the editor for some good hacking.\n",
    "\n",
    "\n",
    "Here a program that uses graphics. These can be notoriously hard to link correctly."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "ade3834a-4887-4678-8955-96799126d652",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MKNEMO> Searching tabplot.c: \n",
      "found one: /home/teuben/NEMO/demo/src/kernel/tab/tabplot.c\n",
      "gcc -g -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -fpic -rdynamic  -Dlinux -DSYSV  -I/home/teuben/NEMO/demo/inc -I/home/teuben/NEMO/demo/lib -I/home/teuben/NEMO/demo/opt/include    -Wall -Wimplicit-function-declaration  -D_GNU_SOURCE -std=c99 -o tabplot tabplot.c \\\n",
      "\t-L/home/teuben/NEMO/demo/lib -L/home/teuben/NEMO/demo/opt/lib          -lnemo -ldl  -lreadline -lhistory -lncurses  -lm  /home/teuben/NEMO/demo/lib/yapp_pgplot.o -L/usr/lib/pgplot5 -lcpgplot -lpgplot    -lSM -lICE -lXext -lX11   -L/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/11/../../.. -lgfortran -lm -lquadmath  -lm\n",
      "\n"
     ]
    }
   ],
   "source": [
    "mknemo tabplot"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4d5ff810-1c91-4323-b344-eba52c12f84f",
   "metadata": {},
   "source": [
    "and a simple benchmark if graphics works in the **tabgen + tabplot** pipe:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "5b1df81b-00b4-4855-8261-7031e82ffbe0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "### nemo Debug Info: read 10 points\n",
      "### nemo Debug Info: min and max value in xcolumns 1: [0.139570 : 0.802354]\n",
      "### nemo Debug Info: min and max value in ycolumns 2,3,4: [0.004308 : 0.988963]\n",
      "### nemo Debug Info: X:min and max value reset to : [0.106431 : 0.835493]\n",
      "### nemo Debug Info: Y:min and max value reset to : [-0.044925 : 1.038196]\n",
      "/home/teuben/NEMO/demo\n",
      "-rw-rw-r-- 1 teuben teuben 4769 Jan 20 15:34 \u001b[0m\u001b[01;35minstalling4.png\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "tabgen - nr=10 nc=4 | tabplot - ycol=2,3,4 point=2,0.1,3,0.2,4,0.3 color=2,3,4 yapp=installing4.png/png\n",
    "pwd\n",
    "ls -l installing4.png"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "06e23405-1225-413e-8469-5e935e27d834",
   "metadata": {},
   "source": [
    "![alt text](installing4.png \"ScatterPlot\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "0d94ba30-5ac9-4838-a642-75cbbe0646c8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Started at:   Mon Jan 20 03:32:36 PM EST 2025\n",
      "Done at:      Mon Jan 20 03:34:41 PM EST 2025\n",
      "300\n"
     ]
    }
   ],
   "source": [
    "date1=$(date)\n",
    "echo \"Started at:   $date0\"\n",
    "echo \"Done at:      $date1\"\n",
    "(cd $NEMOBIN; ls | wc -l)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b475becd-f814-4dd0-9d20-59970896b1c4",
   "metadata": {},
   "source": [
    "How did you do?  Did you get 300 executables in $NEMOBIN, did your install take about 2 minutes?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f92b54f7-0f07-427b-aab0-9e071953a7b0",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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