Differenze

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--- calcoloscientifico:software:python [11/12/2018 14:02] – [Python 3.6.3 virtualenv for "espresso"] roberto.alfieri
+++ calcoloscientifico:software:python [03/08/2021 10:46] (versione attuale) – fabio.spataro
@@ Linea 76: / Linea 76: @@
 <code>
-#MYVE=~/virtualenvironment   # customize here
+#MYVE=~/virtualenvironment # customize here
 MYVE=/hpc/group/T_HPC18A/virtualenvironment
 mkdir -p $MYVE
@@ Linea 91: / Linea 91: @@
 module load gnu/5.4.0
-module load openmpi/1.10.6
+module load openmpi/1.10.7
 module load python/3.6.3
 module load cuda/8.0.61.2
@@ Linea 116: / Linea 116: @@
 </code>
+[[http://espressomd.org/html/doc/installation.html | Installing Espresso ]]
+   cp myconfig-sample.hpp myconfig.hpp
+edit myconfig.php and uncomment defaults ( http://espressomd.org/html/dox/myconfig-default_8hpp_source.html ).
+Then uncomment
+<code>
+/* Virtual sites features */
+#define VIRTUAL_SITES
+//#define VIRTUAL_SITES_RELATIVE
+#define VIRTUAL_SITES_INERTIALESS_TRACERS
+/* Immersed-Boundary Bayreuth version */
+#define IMMERSED_BOUNDARY
+</code>
 <code>
@@ Linea 123: / Linea 140: @@
 --help
-cmake3 \
+ cmake3 -DCMAKE_INSTALL_PREFIX=/hpc/group/T_HPC18A/virtualenvironment/espresso/  -
--DCMAKE_INSTALL_PREFIX="$HOME/local/tools/python/3.6.3/virtualenv/espresso" \
+ DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc -
--DCMAKE_C_COMPILER=/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc \
+  DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/5.4.0/bin/g++ -DWITH_SCAFACOS=OFF .
--DCMAKE_CXX_COMPILER=/opt/ohpc/pub/compiler/gcc/5.4.0/bin/g++ \
--DWITH_SCAFACOS=OFF \
-~/software-build/applications/espresso/4.0/espresso-4.0.0
 </code>
@@ Linea 146: / Linea 160: @@
 <code>
+#!/bin/bash
+#SBATCH --partition=bdw
+#SBATCH --output=%x.o%j
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=4
+#SBATCH --account=T_HPC18A
+module load gnu/5.4.0
+module load openmpi/1.10.7
+module load python/3.6.3
+module load cuda/8.0.61.2
+module load hdf5/1.8.17
+module load gsl/2.2.1
+module load boost/1.63.0
+#activate VE
+source /hpc/group/T_HPC18A/virtualenvironment/espresso/bin/activate
+python /hpc/group/T_HPC18A/software-build/espresso/espresso-4.0.0/samples/immersed_boundary/sampleImmersedBoundary.py
+#deactivate VE
+deactivate
 </code>
@@ Linea 181: / Linea 216: @@
 #SBATCH --nodes=2
 #SBATCH --ntasks-per-node=4
 #SBATCH --account=T_HPC18A
-module load gnu7  openmpi3  py2-mpi4py
+module load gnu7 openmpi3 py2-mpi4py
-#module load intel  openmpi3  py2-mpi4py
+#module load intel openmpi3 py2-mpi4py
-mpirun  python -W ignore hello-mpi-world.py
+mpirun python -W ignore hello-mpi-world.py
 </code>