[gmx-users] Gmx 2016.3 compilation error on PHI

[Jones de Andrade]

Hi all.

I'm having some issues while trying to compile the Gromacs 2016.3 version
for a Xeon Phi Knights *Corner* (not Landing).

I'm running the latest version of cmake (own compilation, worked on other
compilations done previously: 5.1.2 on gcc and 2016.3 on gcc and icc) with
the following line at the moment (sorry for the long paths):

*************
/home/jdandrade/bin/bin/cmake .. -DCMAKE_C_COMPILER=icc
-DCMAKE_CXX_COMPILER=icc -DGMX_FFT_LIBRARY=mkl
-DMKL_LIBRARIES=”/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic:/opt/intel/compilers_and_libraries_2016.1.150/linux/mkl/lib/intel64_lin_mic/”
-DMKL_INCLUDE_DIR=”/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/include/mic:/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/include/intel64”
-DCMAKE_INSTALL_PREFIX=/home/jdandrade/bin -DGMX_BUILD_SHARED_EXE=OFF
-DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/opt/versatushpc/compilers/gnu/5.3/lib64/
-L/opt/versatushpc/compilers/gnu/5.3/lib64/"
-DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi -DGMX_DEFAULT_SUFFIX=OFF
-DGMX_BINARY_SUFFIX=_phi -DGMX_LIBS_SUFFIX=_phi -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_C_FLAGS="-O3 -qopenmp -parallel -ip -mmic" -DCMAKE_CXX_FLAGS="-O3
-qopenmp -parallel -ip -mmic" -DGMX_GPU=OFF
*************

It prepares the compilation fine. When I execute the "make" command it goes
all the way down to 100%, but when it comes to final linking it issues the
following errors:

*************
[100%] Built target mdrun_objlib
Scanning dependencies of target mdrun
[100%] Building CXX object
src/programs/CMakeFiles/mdrun.dir/mdrun_main.cpp.o
[100%] Linking CXX executable ../../bin/mdrun_phi
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.so when searching for
-lcilkrts
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.a when searching for
-lcilkrts
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libcilkrts.so.5 when searching
for libcilkrts.so.5
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libstdc++.so when searching for
-lstdc++
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libgcc_s.so when searching for
-lgcc_s
x86_64-k1om-linux-ld: skipping incompatible
/opt/versatushpc/compilers/gnu/5.3/lib64//libgcc_s.so when searching for
-lgcc_s
*************

As a consequence, when I try to execute the command, using:

gmx grompp -f 1000.BMIm.AlCl4.md.001.mdp -c 1000.BMIm.AlCl4.md.000.gro -p
1000.BMIm.AlCl4.md.top -o 1000.BMIm.AlCl4.md.001.tpr

/usr/bin/micnativeloadex mdrun_phi -a "-nt 32 -ntomp 0 -pin on -s
1000.BMIm.AlCl4.md.001.tpr -o 1000.BMIm.AlCl4.md.001.trr -x
1000.BMIm.AlCl4.md.001.xtc -c 1000.BMIm.AlCl4.md.001.gro -e
1000.BMIm.AlCl4.md.001.edr -g 1000.BMIm.AlCl4.md.001.log -cpo
1000.BMIm.AlCl4.md.001.cpt -nice 0 -v"

I get the following error message:

**************
Dependency information for /home/jdandrade/bin/bin/mdrun_phi

        Full path was resolved as
        /home/jdandrade/bin/bin/mdrun_phi

        Binary was built for Intel(R) Xeon Phi(TM) Coprocessor
        (codename: Knights Corner) architecture

        SINK_LD_LIBRARY_PATH =
/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic/

        Dependencies Found:

/opt/intel/compilers_and_libraries_2016.1.150/linux/compiler/lib/intel64_lin_mic/libiomp5.so

        Dependencies Not Found Locally (but may exist already on the
coprocessor):
                libmkl_intel_lp64.so
                libmkl_sequential.so
                libmkl_core.so
                librt.so.1
                libm.so.6
                libpthread.so.0
                libc.so.6
                libdl.so.2
                libstdc++.so.6
                libgcc_s.so.1
**************

Does anybody has any idea on how to solve this? I would really like to give
phi a try and bench it on my systems.

Thanks a lot in advance.

Jones