diff --git a/.gitignore b/.gitignore index fcb864e..e2531c1 100755 --- a/.gitignore +++ b/.gitignore @@ -34,5 +34,5 @@ output/ # ContainerFiles/ssh id_rsa - +id_rsa.pub diff --git a/ContainerFiles/dev-env.nix b/ContainerFiles/dev-env.nix index 62b60f6..d2957a0 100644 --- a/ContainerFiles/dev-env.nix +++ b/ContainerFiles/dev-env.nix @@ -14,6 +14,7 @@ with import { }; # nix bash + vim # # MPI-related packages @@ -30,4 +31,4 @@ with import { }; # # Refs: # https://stackoverflow.com/questions/46165918/how-to-get-the-name-from-a-nixpkgs-derivation-in-a-nix-expression-to-be-used-by/46173041#46173041 -## \ No newline at end of file +## diff --git a/ContainerFiles/env_backup.drv b/ContainerFiles/env_backup.drv index 07ee7a7..6e6e6fe 100644 --- a/ContainerFiles/env_backup.drv +++ b/ContainerFiles/env_backup.drv @@ -1 +1 @@ -Derive([("out","/nix/store/njmwm90cmzk9mx3pvfv5g0dlqg5yfgaj-openmpi-dev-env","","")],[("/nix/store/10yajwbqfbc1qjsf1k3m6ycpcpvykf3g-nix-2.1.3.drv",["man","out"]),("/nix/store/3xynsfmdjz4ifc27292cxgsnkpqb089a-gfortran-wrapper-7.3.0.drv",["out"]),("/nix/store/6s8iax7fp6j6813nr8kbcjclb18zf7ji-binutils-wrapper-2.30.drv",["out"]),("/nix/store/sv2snvfj65dqh9md4fn1sbin3qx9n7dx-openssh-7.9p1.drv",["out"]),("/nix/store/vsmrpdsq4rmdzbrhhzdf9vffwf4p2sfg-bash-4.4-p23.drv",["out"]),("/nix/store/w4254sxdxdgsbykfzmp6g31pjs32yz1q-perl-5.28.0.drv",["out"]),("/nix/store/x30k04wzg72v9da7zd0ymna05zbzdvlc-stdenv-linux.drv",["out"]),("/nix/store/yxh1vdrhmvv9z9rmkhpdq5vla9gp6bjn-openmpi-3.1.3.drv",["out"]),("/nix/store/zmkbca9m7k4v5k7qvq1s1nc1vjsbsqmf-git-2.19.1.drv",["out"])],["/nix/store/9g4wc31j7a2xp22xpgwr0qssfxahxdzl-builder.pl","/nix/store/9krlzvny65gdc8s7kpb6lkx8cd02c25b-default-builder.sh"],"x86_64-linux","/nix/store/n2hjbpkf4c0m48945ivxs3lmsczzw2rg-bash-4.4-p23/bin/bash",["-e","/nix/store/9krlzvny65gdc8s7kpb6lkx8cd02c25b-default-builder.sh"],[("buildCommand","/nix/store/1dzsd6drn31dgp3hk74x2h87j6jdj55b-perl-5.28.0/bin/perl 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\ No newline at end of file +Derive([("out","/nix/store/rbf7xdpq145w1nzkmf8i9qygiwr520f4-openmpi-dev-env","","")],[("/nix/store/10yajwbqfbc1qjsf1k3m6ycpcpvykf3g-nix-2.1.3.drv",["man","out"]),("/nix/store/3xynsfmdjz4ifc27292cxgsnkpqb089a-gfortran-wrapper-7.3.0.drv",["out"]),("/nix/store/6s8iax7fp6j6813nr8kbcjclb18zf7ji-binutils-wrapper-2.30.drv",["out"]),("/nix/store/i586hfrcqs2z581739skdigdz0dqc1fn-vim-8.1.0490.drv",["out"]),("/nix/store/sv2snvfj65dqh9md4fn1sbin3qx9n7dx-openssh-7.9p1.drv",["out"]),("/nix/store/vsmrpdsq4rmdzbrhhzdf9vffwf4p2sfg-bash-4.4-p23.drv",["out"]),("/nix/store/w4254sxdxdgsbykfzmp6g31pjs32yz1q-perl-5.28.0.drv",["out"]),("/nix/store/x30k04wzg72v9da7zd0ymna05zbzdvlc-stdenv-linux.drv",["out"]),("/nix/store/yxh1vdrhmvv9z9rmkhpdq5vla9gp6bjn-openmpi-3.1.3.drv",["out"]),("/nix/store/zmkbca9m7k4v5k7qvq1s1nc1vjsbsqmf-git-2.19.1.drv",["out"])],["/nix/store/9g4wc31j7a2xp22xpgwr0qssfxahxdzl-builder.pl","/nix/store/9krlzvny65gdc8s7kpb6lkx8cd02c25b-default-builder.sh"],"x86_64-linux","/nix/store/n2hjbpkf4c0m48945ivxs3lmsczzw2rg-bash-4.4-p23/bin/bash",["-e","/nix/store/9krlzvny65gdc8s7kpb6lkx8cd02c25b-default-builder.sh"],[("buildCommand","/nix/store/1dzsd6drn31dgp3hk74x2h87j6jdj55b-perl-5.28.0/bin/perl 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\ No newline at end of file diff --git a/Dockerfile b/Dockerfile index ebb6e18..eb61fb8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,6 @@ -ARG BASEOS -FROM cornellcac/nix_${BASEOS}_base:2cd324f48c57f66d476a7894c6a957a78e49b116 +#ARG BASEOS +#FROM cornellcac/nix_${BASEOS}_base:2cd324f48c57f66d476a7894c6a957a78e49b116 +FROM cornellcac/nix_alpine_base:2cd324f48c57f66d476a7894c6a957a78e49b116 USER root ARG ADDUSER @@ -20,12 +21,17 @@ RUN chown -R $nixuser:$nixuser $HOME/.ssh USER $nixuser RUN $nixenv && cd /tmp && sh $ENVSDIR/persist-env.sh $ENVSDIR/dev-env.nix RUN $nixenv && cd $HOME && \ + eval $(ssh-agent) && \ + ssh-add $HOME/.ssh/id_rsa && \ cat /tmp/bitbucket_ssh_keyscan >> $HOME/.ssh/known_hosts && \ - git clone https://github.com/bernardoct/WaterPaths.git && \ - cd WaterPaths && git checkout 7b380c388c08e9891e345c59125af7b077fd218b && \ + git clone https://github.com/federatedcloud/WaterPaths.git && \ + cd WaterPaths && \ + git checkout aaf3c8ea9755dab072f310ab596cce3d387af8ce && \ nix-shell -I ssh-config-file=./nix/.ssh-standard-config -I ssh-auth-sock=$SSH_AUTH_SOCK nix/shell.nix --run "make borg" && \ rm -f $HOME/.ssh/id_rsa -# + +# Testing +COPY nix/remora.nix $HOME/WaterPaths USER root @@ -46,7 +52,11 @@ RUN SSHD_PATH=$(su -c "$nixenv && nix-build '' --no-build-output --no-o mkdir -p /var/empty/sshd/etc && \ cd /var/empty/sshd/etc && \ ln -s /etc/localtime localtime - + +# make mpi and orted executable symlinks on path +RUN for i in $(ls /nixenv/nixuser/.nix-profile/bin) ; do ln -s /nixenv/nixuser/.nix-profile/bin/"$i" /usr/bin ; done +RUN sed -i 's|^nixuser.*|nixuser:x:1000:1000::/home/nixuser:/nixenv/nixuser/.nix-profile/bin/bash|' /etc/passwd + USER $nixuser @@ -65,6 +75,7 @@ ADD ContainerFiles/ssh/id_rsa.mpi.pub ${SSHDIR}/authorized_keys USER root +RUN passwd -d nixuser RUN chmod -R 600 ${SSHDIR}* && \ chown -R ${nixuser}:${nixuser} ${SSHDIR} diff --git a/README.md b/README.md index 927c539..999d5d7 100644 --- a/README.md +++ b/README.md @@ -73,6 +73,7 @@ source build-docker.sh source docker-compose.sh up --scale mpi_head=1 --scale mpi_node=3 docker exec -u nixuser -it waterpaths_mpi_head_1 /bin/sh cd ~/WaterPaths +nix-shell nix/remora.nix ``` Then you can run with Borg in MPI-mode, e.g.: diff --git a/borgms_hybrid_openmp_mpi.sh b/borgms_hybrid_openmp_mpi.sh index c501db1..5342ab7 100644 --- a/borgms_hybrid_openmp_mpi.sh +++ b/borgms_hybrid_openmp_mpi.sh @@ -1,23 +1,23 @@ #!/bin/bash #PBS -N borgms_run -#PBS -l nodes=24:ppn=16 -#PBS -l walltime=33:00:00 +#PBS -l nodes=2:ppn=16 +#PBS -l walltime=2:00:00 #PBS -o ./output/borgms_run_hybrid.out #PBS -e ./error/borgms_run_hybrid.err # #PBS -m bea # #PBS -M bct52@cornell.edu module load openmpi-1.10.7-gnu-x86_64 -export OMP_NUM_THREADS=16 -N_REALIZATIONS=1000 -DATA_DIR="/scratch/bct52/" +export OMP_NUM_THREADS=4 +N_REALIZATIONS=64 +DATA_DIR=${PBS_O_WORKDIR}/ #"/scratch/bct52/" set -x cd "$PBS_O_WORKDIR" # Construct a copy of the hostfile with only 16 entries per node. # MPI can use this to run 16 tasks on each node. -export TASKS_PER_NODE=1 +export TASKS_PER_NODE=4 uniq "$PBS_NODEFILE"|awk -v TASKS_PER_NODE="$TASKS_PER_NODE" '{for(i=0;i nodefile cat nodefile -mpiexec --hostfile nodefile -n 24 -x OMP_NUM_THREADS ./triangleSimulation -T ${OMP_NUM_THREADS} -t 2344 -r ${N_REALIZATIONS} -d ${DATA_DIR} -C -1 -O rof_tables/ -b true -n 50000 -o 1000 -e 0 +mpiexec --hostfile nodefile -n 8 -x OMP_NUM_THREADS ./triangleSimulation -T ${OMP_NUM_THREADS} -t 2344 -r ${N_REALIZATIONS} -d ${DATA_DIR} -C -1 -O rof_tables_cac/ -b true -n 500 -o 100 -e 0 diff --git a/error/borgms_run_hybrid.err b/error/borgms_run_hybrid.err new file mode 100644 index 0000000..20311cf --- /dev/null +++ b/error/borgms_run_hybrid.err @@ -0,0 +1,8 @@ +ModuleCmd_Load.c(200):ERROR:105: Unable to locate a modulefile for 'vim-8.0' ++ cd /home/fs02/pmr82_0001/bct52/wp_test/WaterPaths ++ export TASKS_PER_NODE=4 ++ TASKS_PER_NODE=4 ++ uniq /var/spool/torque/aux//485311.thecube.cac.cornell.edu ++ awk -v TASKS_PER_NODE=4 '{for(i=0;i {}; +let + mpiP = stdenv.mkDerivation { + name = "mpiP"; + + src = fetchurl { + url = https://sourceforge.net/projects/mpip/files/mpiP/mpiP-3.4.1/mpiP-3.4.1.tar.gz; + sha256 = "1w4n693im81qgbq0m8f0cv8nd8l2h8srriczby8nl7i1fdyz72v8"; + }; + phases = "installPhase"; + + buildInputs = with stdenv; [ binutils gcc gfortran openmpi ]; + + installPhase = '' + mkdir -p $out/ + tar -C $out -xzf $src + + cd $out/mpiP-3.4.1/ + ./configure + make + make install + ''; + }; + remora = stdenv.mkDerivation { + name = "remora"; + + src = fetchurl { + url = https://github.com/TACC/remora/archive/v1.8.3.tar.gz; + sha256 = "08n72i6r8y14zr5wlcllpccv4q9xz6lf0j2d5k7kmyz55qid8kb8"; + }; + phases = "installPhase"; + + buildInputs = with stdenv; [ binutils gcc gfortran openmpi ]; + + installPhase = '' + source $stdenv/setup + + mkdir -p $out/ + tar -C $out -xzf $src + + export REMORA_INSTALL_PREFIX=$out + cd $out/remora-1.8.3 + $out/remora-1.8.3/install.sh + ''; + }; +in +stdenv.mkDerivation { + name = "ProfilingEnv"; + buildInputs = [ + nix + bash + vim + + # MPI-related packages + binutils + gcc + gfortran + openmpi + openssh + + # + # Project code dependencies + # + mpiP + remora + ]; + src = null; + shellHook = '' + export PATH=$PATH:${remora}/bin + export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${remora}/lib + export REMORA_BIN=${remora}/bin + ''; +} diff --git a/nix/shell.nix b/nix/shell.nix index 31a9f00..c211830 100644 --- a/nix/shell.nix +++ b/nix/shell.nix @@ -35,6 +35,7 @@ stdenv.mkDerivation { shellHook = '' mkdir -p ./Borg ln -sfn ${Borg}/include/borgms.h ./Borg/borgms.h + ln -sfn ${Borg}/* ./Borg/ ''; } diff --git a/output/NC_output_MM_S0_N500.set b/output/NC_output_MM_S0_N500.set new file mode 100644 index 0000000..3598aee --- /dev/null +++ b/output/NC_output_MM_S0_N500.set @@ -0,0 +1,45 @@ +0.94742322422597169 0.23021238725008733 0.73112494690719176 0.88041730708289367 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-0,0 +1,621 @@ +compute-1-16 +compute-1-16 +compute-1-16 +compute-1-16 +compute-1-15 +compute-1-15 +compute-1-15 +compute-1-15 +Loading ROF tables +Loading ROF tables +Loading ROF tables +Loading ROF tables +Loading ROF tables +Loading ROF tables +Loading ROF tables +Loading ROF tables +Reading input data. +Reading input data. +Reading input data. +Reading input data. +Reading input data. +Reading input data. +Reading input data. +Reading input data. +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +reading RDM file +Running Borg with: +n_islands: 2 +nfe: 500 +output freq.: 100 +n_weeks: 2344 +n_realizations: 64 + +setting up problem +setting up problem +setting up problem +setting up problem +setting up problem +setting up problem +setting up problem +setting up problem +Reference set will be in /home/fs02/pmr82_0001/bct52/wp_test/WaterPaths//output//NC_output_MM_S0_N500.set. +Runtime files will be in /home/fs02/pmr82_0001/bct52/wp_test/WaterPaths//output//NC_runtime_MM_S0_N500.runtime. +Reference set will be in /home/fs02/pmr82_0001/bct52/wp_test/WaterPaths//output//NC_output_MM_S0_N500.set. +Runtime files will be in 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6.237065 s +Function evaluation time: 6.083191 s +Function evaluation time: 5.868078 s +Function evaluation time: 6.089088 s +Function evaluation time: 6.203706 s +Function evaluation time: 6.156705 s +Function evaluation time: 6.136456 s +Function evaluation time: 6.159628 s +Function evaluation time: 6.557676 s +Function evaluation time: 5.994627 s +Function evaluation time: 5.981788 s +Function evaluation time: 6.585414 s +Function evaluation time: 6.199080 s +Function evaluation time: 6.238736 s +Function evaluation time: 6.133334 s +Function evaluation time: 6.772901 s +Function evaluation time: 6.892096 s +Function evaluation time: 6.081296 s +Function evaluation time: 6.035375 s +Function evaluation time: 6.224191 s +Function evaluation time: 6.250715 s +Function evaluation time: 6.594371 s +Function evaluation time: 6.016465 s +Function evaluation time: 5.994271 s +Function evaluation time: 6.064832 s +Function evaluation time: 6.422679 s +Function evaluation time: 6.823135 s +Function evaluation time: 6.356667 s +Function evaluation time: 6.202370 s +Function evaluation time: 5.931755 s +Function evaluation time: 6.461625 s +Function evaluation time: 6.401208 s +Function evaluation time: 6.567629 s +Function evaluation time: 6.456578 s +Function evaluation time: 6.799076 s +Function evaluation time: 6.945897 s +Function evaluation time: 5.777464 s +Function evaluation time: 6.084076 s +Function evaluation time: 5.989098 s +Function evaluation time: 6.165665 s +Function evaluation time: 6.170009 s +Function evaluation time: 6.310094 s +Function evaluation time: 6.629629 s +Function evaluation time: 5.751819 s +Function evaluation time: 5.977035 s +Function evaluation time: 6.199369 s +Function evaluation time: 6.856901 s +Function evaluation time: 6.332912 s +Function evaluation time: 6.098941 s +Function evaluation time: 6.318056 s +Function evaluation time: 6.135723 s +Function evaluation time: 6.492894 s +Function evaluation time: 6.009919 s +Function evaluation time: 6.122090 s +Function evaluation time: 6.264498 s +Function evaluation time: 6.365967 s +Function evaluation time: 6.436316 s +Function evaluation time: 5.761256 s +Function evaluation time: 6.048369 s +Function evaluation time: 6.037014 s +Function evaluation time: 6.234675 s +Function evaluation time: 6.160872 s +Function evaluation time: 6.212811 s +Function evaluation time: 6.138627 s +Function evaluation time: 5.808894 s +Function evaluation time: 6.233101 s +Function evaluation time: 6.022101 s +Function evaluation time: 6.055999 s +Function evaluation time: 6.216152 s +Function evaluation time: 6.263427 s +Function evaluation time: 6.230301 s +Function evaluation time: 5.954527 s +Function evaluation time: 5.988011 s +Function evaluation time: 6.022753 s +Function evaluation time: 6.055834 s +Function evaluation time: 6.302291 s +Function evaluation time: 5.853803 s +Function evaluation time: 6.200464 s +Function evaluation time: 6.416742 s +Function evaluation time: 6.211499 s +Function evaluation time: 6.181884 s +Function evaluation time: 6.020112 s +Function evaluation time: 5.842803 s +Function evaluation time: 6.591428 s +Function evaluation time: 6.210489 s +Function evaluation time: 6.134308 s +Function evaluation time: 6.216749 s +Function evaluation time: 6.039161 s +Function evaluation time: 5.866495 s +Function evaluation time: 6.251351 s +Function evaluation time: 10.065892 s +Function evaluation time: 6.255241 s +Function evaluation time: 6.204234 s +Function evaluation time: 6.159296 s +Function evaluation time: 6.159688 s +Function evaluation time: 5.821427 s +Function evaluation time: 5.981747 s +Function evaluation time: 6.152476 s +Function evaluation time: 6.695546 s +Function evaluation time: 6.579051 s +Function evaluation time: 6.025437 s +Function evaluation time: 6.336953 s +Function evaluation time: 5.799218 s +Function evaluation time: 6.382259 s +Function evaluation time: 6.311256 s +Function evaluation time: 6.172812 s +Function evaluation time: 6.775920 s +Function evaluation time: 6.483169 s +Function evaluation time: 6.083410 s +Function evaluation time: 6.045089 s +Function evaluation time: 6.123848 s +Function evaluation time: 6.299025 s +Function evaluation time: 6.167722 s +Function evaluation time: 6.580616 s +Function evaluation time: 6.047054 s +Function evaluation time: 5.999585 s +Function evaluation time: 6.185849 s +Function evaluation time: 6.195301 s +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. +master node print, should see only once +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. +Number of failed function evaluations: 0. diff --git a/rof_tables_cac/tables_r0_u0 b/rof_tables_cac/tables_r0_u0 new file mode 100644 index 0000000..7a39ff5 Binary files /dev/null and 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