From 1687c336241d681dbe82a33d4a9c7d7e331c5d83 Mon Sep 17 00:00:00 2001
From: Tru Huynh <tru@pasteur.fr>
Date: Sun, 23 Mar 2025 17:34:07 +0100
Subject: [PATCH] fix $ expansion
---
Dockerfile | 52 ++++++++++++++++++++++++++--------------------------
1 file changed, 26 insertions(+), 26 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 014e5a3..0c436b2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,7 +10,7 @@ V=2024.5
CMAKE=cmake
## GROMACS
cd /opt
-wget -q -O - https://ftp.gromacs.org/gromacs/gromacs-${V}.tar.gz | tar xzvf -
+wget -q -O - https://ftp.gromacs.org/gromacs/gromacs-\${V}.tar.gz | tar xzvf -
cd gromacs-2024.5
mkdir build
cd build
@@ -26,42 +26,42 @@ cmake ../ -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.8 -DGMX_GPU=CUDA \
make -j24 CXXFLAGS="-O3"
make install
-D=/usr/local/gromacs/${V}-openmpi-cuda-12.8.0_570.86.10
+D=/usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10
_build_serial() {
-if [ $# -eq 1 ]; then
+if [ \$# -eq 1 ]; then
OPT=$1
else
exit 1
fi
-mkdir serial-single-precision-${OPT} || :
-(cd serial-single-precision-${OPT} && \
+mkdir serial-single-precision-\${OPT} || :
+(cd serial-single-precision-\${OPT} && \
dpkg -l > dpkg-l
printenv > printenv
-${CMAKE} .. \
+\${CMAKE} .. \
-DGMX_BUILD_OWN_FFTW=ON \
-DREGRESSIONTEST_DOWNLOAD=ON \
--DGMX_SIMD=${OPT} \
--DCMAKE_INSTALL_PREFIX=${D}/serial/single-precision-${OPT}
+-DGMX_SIMD=\${OPT} \
+-DCMAKE_INSTALL_PREFIX=\${D}/serial/single-precision-\${OPT}
nice make -j 16
make check || :
make install
-) 2>&1 | tee -a serial-single-precision-${OPT}.`date '+%Y-%m-%d_%H%M'`
+) 2>&1 | tee -a serial-single-precision-\${OPT}.`date '+%Y-%m-%d_%H%M'`
}
_build_mdrun() {
-if [ $# -eq 1 ]; then
-OPT=$1
+if [ \$# -eq 1 ]; then
+OPT=\$1
else
exit 1
fi
-mkdir mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-${OPT} || :
-(cd mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-${OPT} && \
+mkdir mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT} || :
+(cd mdrun-only-single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT} && \
export CUDACXX=/usr/local/cuda-12.8/bin/nvcc
dpkg -l > dpkg-l
printenv > printenv
-${CMAKE} .. \
+\${CMAKE} .. \
-DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc \
-DGMX_OPENMP=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF \
-DBUILD_SHARED_LIBS=ON \
@@ -69,20 +69,20 @@ ${CMAKE} .. \
-DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-12.8 \
-DGMX_BUILD_MDRUN_ONLY=ON \
-DGMX_GPU=CUDA \
--DGMX_SIMD=${OPT} \
--DCMAKE_INSTALL_PREFIX=${D}/mdrun-only/single-precision-openmpi-cuda-12.8.0_570.86.10-${OPT}
+-DGMX_SIMD=\${OPT} \
+-DCMAKE_INSTALL_PREFIX=\${D}/mdrun-only/single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT}
nice make -j 16 && \
make install
-) 2>&1 | tee -a single-precision-openmpi-cuda-12.8.0_570.86.10-${OPT}.`date '+%Y-%m-%d_%H%M'`
+) 2>&1 | tee -a single-precision-openmpi-cuda-12.8.0_570.86.10-\${OPT}.`date '+%Y-%m-%d_%H%M'`
}
_default_build() {
for i in SSE4.1 AVX_256 AVX2_256 AVX_512
do
-_build_serial $i
-_build_mdrun $i
+_build_serial \$i
+_build_mdrun \$i
done
}
@@ -101,20 +101,20 @@ apt-get clean
# echo first argument must be one of
# echo native
# echo or
-# (cd /usr/local/gromacs/${V}-openmpi-cuda-12.8.0_570.86.10/ && /bin/ls -1d */*)
+# (cd /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/ && /bin/ls -1d */*)
# exit 1
# }
-# if [ $# -ge 1 ]; then
-# if [ "$1" = "native" ]; then
+# if [ \$# -ge 1 ]; then
+# if [ "\$1" = "native" ]; then
# . /usr/local/gromacs-2024.5-openmpi-cuda12.8-native/bin/GMXRC.bash
# else
-# if [ ! -d /usr/local/gromacs/${V}-openmpi-cuda-12.8.0_570.86.10/$1 ] ; then
+# if [ ! -d /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1 ] ; then
# _usage
# fi
-# ls -l /usr/local/gromacs/${V}-openmpi-cuda-12.8.0_570.86.10/$1/bin/GMXRC.bash
-# . /usr/local/gromacs/${V}-openmpi-cuda-12.8.0_570.86.10/$1/bin/GMXRC.bash
+# ls -l /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1/bin/GMXRC.bash
+# . /usr/local/gromacs/\${V}-openmpi-cuda-12.8.0_570.86.10/\$1/bin/GMXRC.bash
# fi
# shift
-# eval "$@"
+# eval "\$@"
# fi
EOF
--
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