{"action":"created","comment":{"url":"https://api.github.com/repos/ofi-cray/fab-utils/pulls/comments/79863697","id":79863697,"diff_hunk":"@@ -0,0 +1,136 @@\n+# Instruction for building and running SNAP\n+\n+Implementation: Fortran, MPI+OpenMPI, uses MPI_THREAD_SERIALIZE\n+\n+Useful links:\n+- GitHub repository: https://github.com/losalamos/SNAP\n+- Useful build and run info: http://www.nersc.gov/users/computational-systems/cori/nersc-8-procurement/trinity-nersc-8-rfp/nersc-8-trinity-benchmarks/snap\n+\n+1. Download from the GitHub repository\n+   ```\n+% git clone https://github.com/losalamos/SNAP.git\n+   ```\n+\n+   README.md in the top level directory contains some useful information\n+\n+2.  Load necessary PrgEnv module, set PATH and LD_LIBRARY_PATH and set\n+recommended environment variables, e.g. for MPICH, etc.\n+\n+3. Modify the Makefile in the `src` directory as necessary.  At most,\n+three changes may be needed.\n+   ```\n+   #FORTRAN = mpif90\n+   #For Gnu and Intel compilers, mpifort works\n+   FORTRAN = mpifort\n+   ```\n+\n+   Select one target. When using GNU, choose `gsnap`; when using Intel\n+   for KNL, choose `ksnap`; when using Intel for non-KNL choose `isnap`.\n+   ```\n+   TARGET = gsnap\n+   #TARGET = isnap\n+   #TARGET = ksnap\n+   ```\n+\n+   If KNL is targeted, specify automatic cpu dispatch so that\n+   executable can run on KNL and non-KNL.\n+   ```\n+   #FFLAGS = -O3 $(OMPFLAG) -xmic-avx512 -ip -align array64byte -qopt-streaming-cache-evict=0 -qno-opt-dynamic-align -fp-model fast -fp-speculation fast -fno-alias -fno-fnalias\n+   FFLAGS = -O3 $(OMPFLAG) -axMIC-AVX512 -ip -align array64byte -qopt-streaming-cache-evict=0 -qno-opt-dynamic-align -fp-model fast -fp-speculation fast -fno-alias -fno-fnalias\n+   ```\n+   \n+4. Build\n+   ```\n+   % make\n+   ```\n+\n+   This creates the above selected executable in the same directory.\n+\n+### Example runs\n+\n+For each example, the number of nodes used can be varied depending on\n+whether Xeon or KNL nodes are used. SNAP requires an input deck which\n+matches the job launch command line with respect to the number of\n+ranks etc.  Thus is is not trivial to modify number of ranks, threads\n+etc. to be used. The user also has to specify an output file which\n+will contain, among other things, performance data.  See\n+[Caveats and other notes](#caveats-and-other-notes) below for more information on how to change\n+these parameters.\n+\n+The following examples refer to inputs files available in this repository.\n+\n+To run small sanity check:\n+```\n+% export OMP_NUM_THREADS=2\n+% export OMP_WAIT_POLICY=passive\n+% srun -n 6 -N 2 --ntasks-per-node=3 -c 4 --threads-per-core 2 --hint=multithread --exclusive <path/exec> 6MT.input <outputfile>\n+```\n+or \n+```\n+% export OMP_NUM_THREADS=2\n+% aprun -n 6 -N 3 -d 2 -cc depth -j 2 <path/exec> 6MT.input <outputfile>\n+```\n+\n+To run NERSC small problem on 96 ranks and 4 nodes:\n+```\n+% export OMP_NUM_THREADS=1\n+% srun -n 96 -N 4 --ntasks-per-node=24 --threads-per-core 1 --exclusive <path/exec> 96ST4nodes.input <outputfile>\n+```\n+   or\n+```\n+% export OMP_NUM_THREADS=1\n+% aprun -n 96 -N 24 <path/exec> 96ST4nodes.input  <outputfile>\n+```\n+\n+To run problem on 512 ranks:\n+```\n+% export OMP_NUM_THREADS=4   # must match input deck, see below\n+% export OMP_WAIT_POLICY=passive\n+% srun -n 512 -N 8 --ntasks-per-node=64 -c 4 --threads-per-core 4 --hint=multithread --exclusive <path/exec> 512MT.input <outputfile>\n+```\n+   or\n+```\n+% export OMP_NUM_THREADS=4   # must match input deck, see below\n+% export OMP_WAIT_POLICY=passive\n+% aprun -n 512 -N 64 -d 4 -cc depth -j 4 <path/exec> ./512MT.input <outputfile>\n+```\n+\n+where `<path/exec>` refers to `gsnap`, `ksnap`, or `isnap`.\n+\n+## Expected output\n+\n+For each run, look for \"Success! Done in a SNAP!\" on stdout to confirm\n+completion.\n+\n+Performance data is summarized at the end in `<outputfile>. In\n+particular look for \"Solve\" time and \"Grind Time\".  Solve time is the","path":"scripts/miniapps/SNAP.md","position":106,"original_position":106,"commit_id":"b3d09283cd20a2936beac214158d741e3c5f7d4b","original_commit_id":"b3d09283cd20a2936beac214158d741e3c5f7d4b","user":{"login":"tonyzinger","id":17089882,"avatar_url":"https://avatars.githubusercontent.com/u/17089882?v=3","gravatar_id":"","url":"https://api.github.com/users/tonyzinger","html_url":"https://github.com/tonyzinger","followers_url":"https://api.github.com/users/tonyzinger/followers","following_url":"https://api.github.com/users/tonyzinger/following{/other_user}","gists_url":"https://api.github.com/users/tonyzinger/gists{/gist_id}","starred_url":"https://api.github.com/users/tonyzinger/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tonyzinger/subscriptions","organizations_url":"https://api.github.com/users/tonyzinger/orgs","repos_url":"https://api.github.com/users/tonyzinger/repos","events_url":"https://api.github.com/users/tonyzinger/events{/privacy}","received_events_url":"https://api.github.com/users/tonyzinger/received_events","type":"User","site_admin":false},"body":"Should the '`' be removed?\r\nWhen looking at this information through the \"View\" file option, \"<outputfile>\" does not appear.  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