I have no idea if this will solve the issue, though for me I had to use "MANUAL" instead of "CLANG" (-DCOMPILER=MANUAL) when defining compilers using environmental variables.
Always something to check at least.
Best regards
// Gustaf
________________________________
Från: Wim R. Cardoen <wcardoen.gmail.com>
Skickat: den 17 juli 2020 22:54:04
Till: amber.ambermd.org
Ämne: [AMBER] Amber20: Error in the linking of the pysander
Hello,
I am trying to compile the Amber code using the Intel compiler on a Centos
7 Box with the following flags.
Compilers & libraries:
---------------------
module purge
module load cmake
module load intel/2017.4.196
Building with cmake:
-------------------
setenv CC icc
setenv CXX icpc
setenv FC ifort
setenv F90 ifort
setenv CFLAGS " -axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2 -fPIC
-I${MKLROOT}/include "
setenv CXXFLAGS "${CFLAGS} "
setenv FFLAGS "${CFLAGS} "
cd /uufs/chpc.utah.edu/sys/installdir/amber/amber20_src/build
# Edit run_cmake:
AMBER_PREFIX=/uufs/chpc.utah.edu/sys/installdir/amber/
cmake $AMBER_PREFIX/amber20_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
-DCOMPILER=INTEL \
-DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE \
-DCHECK_UPDATES=TRUE -DAPPLY_UPDATES=TRUE -DFORCE_EXTERNAL_LIBS=mkl \
2>&1 | tee cmake.log
./run_cmake
make -j 6 install
The build (linking the Python package) fails due to invoking gcc with the
wrong flags i.e. Intel Compiler flags.
(see below)
Any suggestions?
Thanks,
Wim
icc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
-axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2 -fPIC -I/uufs/
chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2017.4.196/linux/mkl/include
-fPIC -I/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/AmberTools/src/include
-I/uufs/chpc.utah.edu/sys/installdir/amber/amber20_src/AmberTools/src/sander
-I/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.7m
-c sander/src/pysandermodule.c -o /uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-3.7/sander/src/pysandermodule.o
sander/src/pysandermodule.c(39): (col. 48) remark: pysander_setup has been
targeted for automatic cpu dispatch
gcc -pthread -shared -B /uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/CMakeFiles/miniconda/install/compiler_compat
-L/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/CMakeFiles/miniconda/install/lib
-Wl,-rpath=/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/CMakeFiles/miniconda/install/lib
-Wl,--no-as-needed -Wl,--sysroot=/ -axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O2
-fPIC -I/uufs/
chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2017.4.196/linux/mkl/include
/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/temp.linux-x86_64-3.7/sander/src/pysandermodule.o
-L/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/AmberTools/src/sander
-L/uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/AmberTools/src/sander
-lsander -o /uufs/
chpc.utah.edu/sys/installdir/amber/amber20_src/build/AmberTools/src/pysander/CMakeFiles/pysander-build/lib.linux-x86_64-3.7/sander/pysander.cpython-37m-x86_64-linux-gnu.so
gcc: error: unrecognized command line option
‘-axCORE-AVX512,CORE-AVX2,AVX,SSE4.2’
error: command 'gcc' failed with exit status 1
make[2]: ***
[AmberTools/src/pysander/CMakeFiles/pysander-build/pysander-build.stamp]
Error 1
make[1]: *** [AmberTools/src/pysander/CMakeFiles/pysander.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[100%] Built target cpptraj
make: *** [all] Error 2
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 18 2020 - 13:00:03 PDT
