From d88da3507acd85ba50eb795cf2f3ed0661ac39e9 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Fri, 22 Apr 2022 18:56:39 -0400 Subject: [PATCH 1/8] Stop ignoring env/ --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 516933e..3063953 100644 --- a/.gitignore +++ b/.gitignore @@ -104,7 +104,6 @@ celerybeat.pid # Environments .env .venv -env/ venv/ ENV/ env.bak/ From 90ad5137b2a386e58eafd3c92489fb709e4a0a14 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Fri, 22 Apr 2022 18:58:14 -0400 Subject: [PATCH 2/8] Add install scripts for Summit --- install/env/summit.sh | 7 +++++++ install/summit.sh | 42 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100755 install/env/summit.sh create mode 100755 install/summit.sh diff --git a/install/env/summit.sh b/install/env/summit.sh new file mode 100755 index 0000000..ad6b094 --- /dev/null +++ b/install/env/summit.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +. /etc/profile + +module load gcc +module load cmake +module load open-ce/1.5.2 diff --git a/install/summit.sh b/install/summit.sh new file mode 100755 index 0000000..d7def46 --- /dev/null +++ b/install/summit.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +. /etc/profile + +module load cmake +module load open-ce/1.5.2 + +conda create -p dhenv --clone base -y +conda activate dhenv/ + +# Clone DeepHyper (develop) +git clone -b develop https://github.com/deephyper/deephyper.git + +# Clone DeepHyper/Scikit-Optimize (master) +git clone https://github.com/deephyper/scikit-optimize.git + +# Clone Plasma Fork (tf2) +git clone -b tf2 https://github.com/deephyper/plasma-python.git + +# Install DeepHyper +pip install -e deephyper/ +pip install -e scikit-optimize/ +pip install -e plasma-python/ + +# Install Scalable-BO +pip install -e ../src/scalbo/ + +# Install mpi4py +git clone https://github.com/mpi4py/mpi4py.git +cd mpi4py/ + +module load gcc + +MPICC=mpicc python setup.py install +cd .. + +# Install rdkit +####pip install rdkit-pypi + +# Copy activation of environment file +cp ../install/env/summit.sh activate-dhenv.sh +echo "conda activate $PWD/dhenv/" >> activate-dhenv.sh From 29009102d582ef4c3e73acf0ad2f43430955e33b Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Mon, 9 May 2022 22:37:31 -0400 Subject: [PATCH 3/8] Add Summit counterpart for minimalistic-frnn-test.sh Fix clone of base OpenCE env --- .../summit/jobs/minimalistic-frnn-test.sh | 25 +++++++++++++++++++ install/summit.sh | 2 +- 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100755 experiments/summit/jobs/minimalistic-frnn-test.sh diff --git a/experiments/summit/jobs/minimalistic-frnn-test.sh b/experiments/summit/jobs/minimalistic-frnn-test.sh new file mode 100755 index 0000000..e7bbd19 --- /dev/null +++ b/experiments/summit/jobs/minimalistic-frnn-test.sh @@ -0,0 +1,25 @@ +#!/bin/bash +#BSUB -nnodes 1 +#BSUB -W 2:20 +#BSUB -q debug +#BSUB -P fus145 + +# https://docs.olcf.ornl.gov/systems/summit_user_guide.html#common-bsub-options + +source ../../../build/activate-dhenv.sh + +export RANKS_PER_NODE=1 +export NUM_NODES=1 +export PYTHONPATH=../../../build/dhenv/lib/python3.7/site-packages/:$PYTHONPATH + +# man jsrun +# · -E , –env var=value Exports the specified environment variable to the started processes before the +# program is run. This option overrides any locally defined environment variable with the same name. +# Existing environment variables can be propagated or new variables can be exported with corresponding +# values. For example, jsrun -E OMP_NUM_THREADS=4 -E PROG_INPUT. + +# · -F , –env_eval var=val Evaluates the environment variable in the remote environment and sets the envi‐ +# ronment variable in the environment of the started processes. + +echo "Running: jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) python -m scalbo.benchmark.minimalistic_frnn" +jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) python -m scalbo.benchmark.minimalistic_frnn diff --git a/install/summit.sh b/install/summit.sh index d7def46..4b5459d 100755 --- a/install/summit.sh +++ b/install/summit.sh @@ -5,7 +5,7 @@ module load cmake module load open-ce/1.5.2 -conda create -p dhenv --clone base -y +conda create -p dhenv --clone open-ce-1.5.2-py39-0 -y conda activate dhenv/ # Clone DeepHyper (develop) From 8096bdfacabe99d920eee03d80cad86d42c30a57 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Mon, 9 May 2022 22:17:50 -0500 Subject: [PATCH 4/8] Add instructions for Summit --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index 093569c..5161d4d 100644 --- a/README.md +++ b/README.md @@ -95,6 +95,13 @@ From the `scalable-bo/build` folder, execute the following commands: ```console ../install/thetagpu.sh ``` +### For Summit (OLCF) + +From the `scalable-bo/build` folder, execute the following commands: + +```console +../install/summit.sh +``` ## Organization of the repository @@ -209,3 +216,9 @@ cd experiments/theta/jobs/ cd experiments/thetagpu/jobs/ ``` + +### For Summit (OLCF) + +```console +cd experiments/summit/jobs/ +``` From 6bc0b20d0cdeaf4ccfbd91f45acee7f6b257c293 Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Mon, 9 May 2022 23:30:43 -0400 Subject: [PATCH 5/8] Use Python 3.7 not 3.9 --- install/summit.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install/summit.sh b/install/summit.sh index 4b5459d..8d7f8ee 100755 --- a/install/summit.sh +++ b/install/summit.sh @@ -5,7 +5,7 @@ module load cmake module load open-ce/1.5.2 -conda create -p dhenv --clone open-ce-1.5.2-py39-0 -y +conda create -p dhenv --clone open-ce-1.5.2-py37-0 -y conda activate dhenv/ # Clone DeepHyper (develop) From af7eeb8f53e4292479cb64c7ef47a6103a755d9e Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Tue, 10 May 2022 01:05:15 -0400 Subject: [PATCH 6/8] Pin module load to Python 3.7 --- install/env/summit.sh | 2 +- install/summit.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/install/env/summit.sh b/install/env/summit.sh index ad6b094..76d7315 100755 --- a/install/env/summit.sh +++ b/install/env/summit.sh @@ -4,4 +4,4 @@ module load gcc module load cmake -module load open-ce/1.5.2 +module load open-ce/1.5.2-py37-0 diff --git a/install/summit.sh b/install/summit.sh index 8d7f8ee..56f3cb0 100755 --- a/install/summit.sh +++ b/install/summit.sh @@ -3,7 +3,7 @@ . /etc/profile module load cmake -module load open-ce/1.5.2 +module load open-ce/1.5.2-py37-0 conda create -p dhenv --clone open-ce-1.5.2-py37-0 -y conda activate dhenv/ From 6223aec79969816de0da3a62564d8610636b43df Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Fri, 24 Jun 2022 15:36:37 -0400 Subject: [PATCH 7/8] Switch to Python 3.8 OpenCE on Summit --- .../summit/jobs/minimalistic-frnn-test.sh | 19 ++++++++----------- install/env/summit.sh | 2 +- install/summit.sh | 10 +++++++--- 3 files changed, 16 insertions(+), 15 deletions(-) diff --git a/experiments/summit/jobs/minimalistic-frnn-test.sh b/experiments/summit/jobs/minimalistic-frnn-test.sh index e7bbd19..b3c8945 100755 --- a/experiments/summit/jobs/minimalistic-frnn-test.sh +++ b/experiments/summit/jobs/minimalistic-frnn-test.sh @@ -1,6 +1,6 @@ #!/bin/bash #BSUB -nnodes 1 -#BSUB -W 2:20 +#BSUB -W 2:00 #BSUB -q debug #BSUB -P fus145 @@ -10,16 +10,13 @@ source ../../../build/activate-dhenv.sh export RANKS_PER_NODE=1 export NUM_NODES=1 -export PYTHONPATH=../../../build/dhenv/lib/python3.7/site-packages/:$PYTHONPATH +export PYTHONPATH=../../../build/dhenv/lib/python3.8/site-packages/:$PYTHONPATH -# man jsrun -# · -E , –env var=value Exports the specified environment variable to the started processes before the -# program is run. This option overrides any locally defined environment variable with the same name. -# Existing environment variables can be propagated or new variables can be exported with corresponding -# values. For example, jsrun -E OMP_NUM_THREADS=4 -E PROG_INPUT. - -# · -F , –env_eval var=val Evaluates the environment variable in the remote environment and sets the envi‐ -# ronment variable in the environment of the started processes. +which python +echo $PATH echo "Running: jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) python -m scalbo.benchmark.minimalistic_frnn" -jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) python -m scalbo.benchmark.minimalistic_frnn +jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) -r1 -g6 -a1 -c42 -bpacked:42 which python +jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) -r1 -g6 -a1 -c42 -bpacked:42 printenv +jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) -r1 -g6 -a1 -c42 -bpacked:42 python -c "import scalbo; print(scalbo.__path__)" +jsrun -E LD_LIBRARY_PATH -E PYTHONPATH -E PATH -n $(( $NUM_NODES * $RANKS_PER_NODE )) -r1 -g6 -a1 -c42 -bpacked:42 python -m scalbo.benchmark.minimalistic_frnn diff --git a/install/env/summit.sh b/install/env/summit.sh index 76d7315..b1781d0 100755 --- a/install/env/summit.sh +++ b/install/env/summit.sh @@ -4,4 +4,4 @@ module load gcc module load cmake -module load open-ce/1.5.2-py37-0 +module load open-ce/1.5.2-py38-0 diff --git a/install/summit.sh b/install/summit.sh index 56f3cb0..b0f7af5 100755 --- a/install/summit.sh +++ b/install/summit.sh @@ -1,11 +1,15 @@ #!/bin/bash -. /etc/profile +# . /etc/profile + +set -e module load cmake -module load open-ce/1.5.2-py37-0 +module load open-ce/1.5.0-py38-0 +#module load open-ce -conda create -p dhenv --clone open-ce-1.5.2-py37-0 -y +conda create -p dhenv --clone open-ce-1.5.0-py38-0 -y +#conda create -p dhenv --clone open-ce-1.5.2-py39-0 -y conda activate dhenv/ # Clone DeepHyper (develop) From ca61712d0a45410a8be986017c6f96c1c783cc9f Mon Sep 17 00:00:00 2001 From: Kyle Gerard Felker Date: Thu, 14 Jul 2022 11:41:20 -0500 Subject: [PATCH 8/8] Need to source /etc/profile to get module shell cmd Was previously source /etc/bashrc in ~/.bashenv, which accomplished the same result, but broke jsrun+xalt --- install/summit.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install/summit.sh b/install/summit.sh index b0f7af5..b74c7c8 100755 --- a/install/summit.sh +++ b/install/summit.sh @@ -1,6 +1,6 @@ #!/bin/bash -# . /etc/profile +. /etc/profile set -e