Merge pull request #73 from pyiron/env

use PYIRON_CORES and PYIRON_THREADS
pyiron · Jun 28, 2024 · aba8b8e · aba8b8e
2 parents 9ff7207 + bacc265
commit aba8b8e
Show file tree

Hide file tree

Showing 30 changed files with 25 additions and 33 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -44,7 +44,6 @@ jobs:
         mv ../thermodynamics resources
         mv ../LICENSE resources
         mv ../damask resources
-        mv ../templates resources
         mkdir resources/lammps/potentials
         mv iprpy-data/share/iprpy/potentials_lammps.csv resources/lammps/potentials/potentials_lammps.csv
         mv iprpy-data/share/iprpy/potential_LAMMPS resources/lammps/potentials/potential_LAMMPS

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -43,7 +43,6 @@ jobs:
         mv ../thermodynamics resources
         mv ../LICENSE resources
         mv ../damask resources
-        mv ../templates resources
         mkdir resources/lammps/potentials
         mv iprpy-data/share/iprpy/potentials_lammps.csv resources/lammps/potentials/potentials_lammps.csv
         mv iprpy-data/share/iprpy/potential_LAMMPS resources/lammps/potentials/potential_LAMMPS

diff --git a/damask/bin/run_damask_3.0.0.sh b/damask/bin/run_damask_3.0.0.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-export OMP_NUM_THREADS=1
+export OMP_NUM_THREADS="${PYIRON_CORES:=1}"
 DAMASK_grid -m material.yaml -l loading.yaml -g damask.vti
diff --git a/damask/bin/run_damask_3.0.0_mpi.sh b/damask/bin/run_damask_3.0.0_mpi.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
-export OMP_NUM_THREADS=$1
+export OMP_NUM_THREADS="${PYIRON_CORES:=$1}"
 DAMASK_grid -m material.yaml -l loading.yaml -g damask.vti
diff --git a/lammps/bin/run_lammps_2020.03.03.sh b/lammps/bin/run_lammps_2020.03.03.sh
diff --git a/lammps/bin/run_lammps_2020.03.03_mpi.sh b/lammps/bin/run_lammps_2020.03.03_mpi.sh
diff --git a/lammps/bin/run_lammps_2024.02.07.sh b/lammps/bin/run_lammps_2024.02.07.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=1} --oversubscribe lmp_mpi -in control.inp;
diff --git a/lammps/bin/run_lammps_2024.02.07_mpi.sh b/lammps/bin/run_lammps_2024.02.07_mpi.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=$1} --oversubscribe lmp_mpi -in control.inp;
diff --git a/mlip/bin/run_lammpsmlip_2020.12.24.sh b/mlip/bin/run_lammpsmlip_2020.12.24.sh
@@ -1,2 +1,2 @@
 #!/bin/bash
-mpiexec -n 1 lmp_mpi -in control.inp
+mpiexec -n ${PYIRON_CORES:=1} lmp_mpi -in control.inp
diff --git a/mlip/bin/run_lammpsmlip_2020.12.24_mpi.sh b/mlip/bin/run_lammpsmlip_2020.12.24_mpi.sh
@@ -1,2 +1,2 @@
 #!/bin/bash
-mpiexec -n $1 lmp_mpi -in control.inp
+mpiexec -n ${PYIRON_CORES:=$1} lmp_mpi -in control.inp
diff --git a/mlip/bin/run_mlip_1.0.0_mpi.sh b/mlip/bin/run_mlip_1.0.0_mpi.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-export MLP_COMMAND_PARALLEL="mpiexec -n $1 mlp"
+export MLP_COMMAND_PARALLEL="mpiexec -n ${PYIRON_CORES:=$1} mlp"
 export MLP_COMMAND_SERIAL="mlp"
 
 chmod +x mlip.sh

diff --git a/mlip/bin/run_mlipjob_1.0.0_mpi.sh b/mlip/bin/run_mlipjob_1.0.0_mpi.sh
@@ -1,2 +1,2 @@
 #!/bin/bash
-mpiexec -n $1 mlp run mlip.ini --filename=structure.cfg
+mpiexec -n ${PYIRON_CORES:=$1} mlp run mlip.ini --filename=structure.cfg
diff --git a/quantumespresso/bin/run_quantumespresso_6.3.sh b/quantumespresso/bin/run_quantumespresso_6.3.sh
@@ -2,4 +2,4 @@
 # DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 # export ESPRESSO_PSEUDO=${DIR}/../potentials
 export ESPRESSO_PSEUDO=${CONDA_PREFIX}/share/pslibrary/pbe/PSEUDOPOTENTIALS/
-mpirun -np 1 pw.x -in pyiron.pwi > pyiron.pwo
+mpirun -np ${PYIRON_CORES:=1} pw.x -in pyiron.pwi > pyiron.pwo
diff --git a/quantumespresso/bin/run_quantumespresso_6.3_mpi.sh b/quantumespresso/bin/run_quantumespresso_6.3_mpi.sh
@@ -2,4 +2,4 @@
 # DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 # export ESPRESSO_PSEUDO=${DIR}/../potentials
 export ESPRESSO_PSEUDO=${CONDA_PREFIX}/share/pslibrary/pbe/PSEUDOPOTENTIALS/
-mpirun -np ${1} pw.x -in pyiron.pwi > pyiron.pwo
+mpirun -np ${PYIRON_CORES:=$1} pw.x -in pyiron.pwi > pyiron.pwo
diff --git a/sphinx/bin/run_sphinx_2.6.1.sh → sphinx/bin/run_sphinx_3.1.sh b/sphinx/bin/run_sphinx_2.6.1.sh → sphinx/bin/run_sphinx_3.1.sh
diff --git a/sphinx/bin/run_sphinx_2.6.1_mpi.sh → sphinx/bin/run_sphinx_3.1_mpi.sh b/sphinx/bin/run_sphinx_2.6.1_mpi.sh → sphinx/bin/run_sphinx_3.1_mpi.sh
@@ -8,8 +8,12 @@ if [ ! -z $2 ]; then
 	SX_THREADS=$2
 	NCORES=$(echo "$1/$SX_THREADS" | bc)
 	export SX_THREADS
+elif [ ! -z $PYIRON_THREADS ]; then
+	SX_THREADS=$PYIRON_THREADS
+	NCORES=$(echo "$PYIRON_CORES/$SX_THREADS" | bc)
+        export SX_THREADS
 else
-	NCORES=$1
+	NCORES="${PYIRON_CORES:=$1}"
 fi
 mpiexec -n $NCORES sphinx --opts > sphinx.log
 mpiexec -n $NCORES sphinx >> sphinx.log

diff --git a/templates/DemoScriptJob/input.json b/templates/DemoScriptJob/input.json
diff --git a/templates/DemoScriptJob/script.py b/templates/DemoScriptJob/script.py
diff --git a/vasp/bin/run_vasp_5.4.4_default_mpi.sh b/vasp/bin/run_vasp_5.4.4_default_mpi.sh
diff --git a/vasp/bin/run_vasp_5.4.4_gam_mpi.sh b/vasp/bin/run_vasp_5.4.4_gam_mpi.sh
diff --git a/vasp/bin/run_vasp_5.4.4_ncl_mpi.sh b/vasp/bin/run_vasp_5.4.4_ncl_mpi.sh
diff --git a/vasp/bin/run_vasp_5.4.4_std_mpi.sh b/vasp/bin/run_vasp_5.4.4_std_mpi.sh
diff --git a/vasp/bin/run_vasp_5.4.4_default.sh → vasp/bin/run_vasp_6.4.3_default.sh b/vasp/bin/run_vasp_5.4.4_default.sh → vasp/bin/run_vasp_6.4.3_default.sh
diff --git a/vasp/bin/run_vasp_6.4.3_default_mpi.sh b/vasp/bin/run_vasp_6.4.3_default_mpi.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=$1} vasp_std
diff --git a/vasp/bin/run_vasp_5.4.4_gam.sh → vasp/bin/run_vasp_6.4.3_gam.sh b/vasp/bin/run_vasp_5.4.4_gam.sh → vasp/bin/run_vasp_6.4.3_gam.sh
diff --git a/vasp/bin/run_vasp_6.4.3_gam_mpi.sh b/vasp/bin/run_vasp_6.4.3_gam_mpi.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=$1} vasp_gam
diff --git a/vasp/bin/run_vasp_5.4.4_ncl.sh → vasp/bin/run_vasp_6.4.3_ncl.sh b/vasp/bin/run_vasp_5.4.4_ncl.sh → vasp/bin/run_vasp_6.4.3_ncl.sh
diff --git a/vasp/bin/run_vasp_6.4.3_ncl_mpi.sh b/vasp/bin/run_vasp_6.4.3_ncl_mpi.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=$1} vasp_ncl
diff --git a/vasp/bin/run_vasp_5.4.4_std.sh → vasp/bin/run_vasp_6.4.3_std.sh b/vasp/bin/run_vasp_5.4.4_std.sh → vasp/bin/run_vasp_6.4.3_std.sh
diff --git a/vasp/bin/run_vasp_6.4.3_std_mpi.sh b/vasp/bin/run_vasp_6.4.3_std_mpi.sh
@@ -0,0 +1,2 @@
+#!/bin/bash
+mpiexec -n ${PYIRON_CORES:=$1} vasp_std
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		mpiexec -n ${PYIRON_CORES:=1} --oversubscribe lmp_mpi -in control.inp;
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		mpiexec -n ${PYIRON_CORES:=$1} --oversubscribe lmp_mpi -in control.inp;
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		mpiexec -n ${PYIRON_CORES:=$1} vasp_std
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		mpiexec -n ${PYIRON_CORES:=$1} vasp_gam
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#!/bin/bash
		mpiexec -n ${PYIRON_CORES:=$1} vasp_ncl