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--- calcoloscientifico:software:python [11/12/2018 13:55] – [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 114: / Linea 114: @@
 Installing collected packages: urllib3, idna, chardet, certifi, requests, docutils, snowballstemmer, pytz, babel, MarkupSafe, Jinja2, sphinxcontrib-websupport, six, Pygments, pyparsing, packaging, alabaster, imagesize, sphinx, latexcodec, PyYAML, pybtex, pybtex-docutils, oset, sphinxcontrib-bibtex, numpy, biopython, decorator, networkx, GridDataFormats, msgpack, mmtf-python, joblib, scipy, cycler, python-dateutil, kiwisolver, matplotlib, pbr, mock, gsd, MDAnalysis
 Successfully installed GridDataFormats-0.4.0 Jinja2-2.10 MDAnalysis-0.19.2 MarkupSafe-1.1.0 PyYAML-3.13 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 biopython-1.72 certifi-2018.10.15 chardet-3.0.4 cycler-0.10.0 decorator-4.3.0 docutils-0.14 gsd-1.5.4 idna-2.7 imagesize-1.1.0 joblib-0.13.0 kiwisolver-1.0.1 latexcodec-1.0.5 matplotlib-3.0.2 mmtf-python-1.1.2 mock-2.0.0 msgpack-0.5.6 networkx-2.2 numpy-1.15.4 oset-0.1.3 packaging-18.0 pbr-5.1.1 pybtex-0.22.0 pybtex-docutils-0.2.1 pyparsing-2.3.0 python-dateutil-2.7.5 pytz-2018.7 requests-2.20.1 scipy-1.1.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.8.2 sphinxcontrib-bibtex-0.4.0 sphinxcontrib-websupport-1.1.0 urllib3-1.24.1
+</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>
 cmake3 \
 ~/software-build/applications/espresso/4.0/espresso-4.0.0 \
 --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>
+Build files have been written to: /hpc/group/T_HPC18A/software-build/espresso/espresso-4.0.0
+Installing: /hpc/group/T_HPC18A/virtualenvironment/espresso/
 Compile and install in the VE
@@ Linea 135: / Linea 157: @@
   deactivate
+Slurm script espresso.sh
+<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>
 ==== MPI for PYTHON ====
@@ Linea 168: / 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>