[gmx-users] gromacs 4.6.7 plumed -Segmentation fault
Ana Marija
sokovic.anamarija at gmail.com
Fri Oct 23 19:52:20 CEST 2015
after cmake step I got this:
CMake Warning:
Manually-specified variables were not used by the project:
BUILD_SHARED_EXE
GMX_BUILD_SHARED_EXE
GMX_FORCE_CXX
MPI_LIBRARY
my cmake was this:
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
-DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
-DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
-DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
-DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
-DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
-DCMAKE_SKIP_RPATH=ON -DBUILD_SHARED_EXE=OFF -DGMX_BUILD_SHARED_EXE=OFF
can you please let me know what I am doing wrong?
On Fri, Oct 23, 2015 at 12:06 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> I don't know what's going to work. Every machine is precious individual
> snowflake. Try it :-)
>
> Mark
>
> On Fri, Oct 23, 2015 at 7:04 PM Ana Marija <sokovic.anamarija at gmail.com>
> wrote:
>
>> thanks, I do I need to set?
>>
>> export CFLAGS="-static"
>> export CXXFLAGS="-static"
>>
>> before cmake step?
>>
>> On Fri, Oct 23, 2015 at 12:03 PM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I think -DGMX_BUILD_SHARED_EXE=off is supposed to handle this - see
>>> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#static-linking.
>>> Or there are environment variables you can set that force the Cray tools to
>>> do dynamic vs static linking - check your local docs.
>>>
>>> As you can see on that Redmine, we're trying to get Cray to be useful
>>> solving these problems in a general way, but progress is slow :-(
>>>
>>> Mark
>>>
>>> On Fri, Oct 23, 2015 at 6:17 PM Ana Marija <sokovic.anamarija at gmail.com>
>>> wrote:
>>>
>>>> or should I do just this before cmake step?
>>>>
>>>> export CFLAGS="-static"
>>>> export CXXFLAGS="-static"
>>>>
>>>>
>>>>
>>>> On Fri, Oct 23, 2015 at 11:12 AM, Ana Marija <
>>>> sokovic.anamarija at gmail.com> wrote:
>>>>
>>>>> the above was reported here as a bug, but I am not sure where and how
>>>>> should I put this flag: CFLAGS=CXXFLAGS=-static
>>>>>
>>>>> http://redmine.gromacs.org/issues/1641
>>>>>
>>>>> does is just go under cmake like: -DCFLAGS=CXXFLAGS=-static or?
>>>>>
>>>>> On Fri, Oct 23, 2015 at 10:51 AM, Ana Marija <
>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>
>>>>>> HI Everybody,
>>>>>>
>>>>>> I got cmake/3.3.2 installed so I decided to install gromacs 5.0.4
>>>>>> with plumed 2.2.0
>>>>>>
>>>>>> but I got this error during "make" step of gromacs:
>>>>>>
>>>>>> 100%] Linking CXX executable ../../bin/gmx_mpi
>>>>>> /usr/lib/../lib64/librt.a(clock_gettime.o): In function
>>>>>> `hp_timing_gettime':
>>>>>> /usr/src/packages/BUILD/glibc-2.11.3/rt/../sysdeps/unix/clock_gettime.c:65:
>>>>>> undefined reference to `_dl_cpuclock_offset'
>>>>>> collect2: error: ld returned 1 exit status
>>>>>> make[2]: *** [bin/gmx_mpi] Error 1
>>>>>> make[1]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
>>>>>>
>>>>>> my recipe is bellow and I am doing this on Cray XE6 machine, please
>>>>>> let me know what I can be doing wrong:
>>>>>>
>>>>>> module swap PrgEnv-cray PrgEnv-gnu
>>>>>> module load fftw/3.3.4.0
>>>>>> module load cray-mpich/7.0.5
>>>>>> module load gsl/1.15
>>>>>> module load cmake
>>>>>> #in /lustre/beagle2/ams/new/gromacs make directory lib2
>>>>>>
>>>>>> mkdir lib2
>>>>>>
>>>>>> ams at login1:/lustre/beagle2/ams/lib2>ln -s
>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>>>>> ams at login1:/lustre/beagle2/ams/lib2>ln -s
>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>>>>>
>>>>>> #download it from here: http://www.plumed-code.org/get-it
>>>>>> tar zxvf plumed-2.2.0.tgz
>>>>>> cd plumed-2.2.0
>>>>>>
>>>>>> ./configure CC=cc CXX=CC F77=ftn
>>>>>> LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
>>>>>> --prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
>>>>>> --disable-basic-warnings --disable-openmp
>>>>>>
>>>>>> <strong>###Makefile.conf should look like this, if not please delete
>>>>>> all extra stuff before proceeding to make step</strong>
>>>>>> CC=cc
>>>>>> FC=gfortran
>>>>>> LDF90=gfortran
>>>>>> CFLAGS=-g -O2 -fPIC
>>>>>> CXX=CC
>>>>>> CXXFLAGS=-O -fPIC
>>>>>> CXXFLAGS_NOOPENMP=-O -fPIC
>>>>>> CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
>>>>>> -DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
>>>>>> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
>>>>>> -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
>>>>>> -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
>>>>>> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
>>>>>> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
>>>>>> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
>>>>>> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
>>>>>> -D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
>>>>>> -D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
>>>>>> LDFLAGS=
>>>>>> DYNAMIC_LIBS=-lstdc++ -lz -ldl -L/lustre/beagle2/ams/new/gromacs/lib2
>>>>>> LIBS=-ldl
>>>>>> SOEXT=
>>>>>> LD=CC
>>>>>> LDSO=CC -shared
>>>>>> GCCDEP=CC
>>>>>> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
>>>>>> program_transform_name=s,x,x,
>>>>>> program_can_run_mpi=yes
>>>>>> program_can_run=yes
>>>>>> LD_RO=ld -r -o
>>>>>> exec_prefix=${prefix}
>>>>>> bindir=${exec_prefix}/bin
>>>>>> libdir=${exec_prefix}/lib
>>>>>> includedir=${prefix}/include
>>>>>> datarootdir=${prefix}/share
>>>>>> datadir=${datarootdir}
>>>>>> docdir=${datarootdir}/doc/plumed
>>>>>> htmldir=${docdir}
>>>>>> program_name=plumed
>>>>>> ###
>>>>>>
>>>>>> make
>>>>>> make install
>>>>>>
>>>>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>>>>
>>>>>> #1. Make a directory for modulefiles (e.g.
>>>>>> /lustre/beagle2/ams/new/modulefiles/)
>>>>>> #2. Copy file: cp
>>>>>> /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile
>>>>>> /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/
>>>>>> #3. type "module use /lustre/beagle2/ams/new/modulefiles/"
>>>>>> #4. type "module load plumed/2.2.0"
>>>>>>
>>>>>> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>>>>>> module use /lustre/beagle2/ams/new/modulefiles/
>>>>>> module load plumed/2.2.0
>>>>>>
>>>>>> ### instal gromacs-5.0.4
>>>>>> wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.4.tar.gz
>>>>>> tar zxvf gromacs-5.0.4.tar.gz
>>>>>> cd gromacs-5.0.4/
>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4>plumed-patch
>>>>>> -p --static
>>>>>>
>>>>>>
>>>>>> PLUMED patching tool
>>>>>>
>>>>>> 1) amber14 4) gromacs-5.0.4 7) namd-2.8
>>>>>> 2) gromacs-4.5.7 5) gromacs-5.1.0 8) namd-2.9
>>>>>> 3) gromacs-4.6.7 6) lammps-6Apr13 9) qespresso-5.0.2
>>>>>>
>>>>>> Choose the best matching code/version:4
>>>>>>
>>>>>> mkdir build
>>>>>> cd build
>>>>>>
>>>>>>
>>>>>> export BUILD_WITH_INSTALL_RPATH=TRUE
>>>>>> export INSTALL_RPATH=""
>>>>>> export SKIP_BUILD_RPATH=TRUE
>>>>>> export
>>>>>> CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/new/gromacs/lib:$CMAKE_LIBRARY_PATH"
>>>>>>
>>>>>> #in /lustre/beagle2/ams/new/gromacs make directory lib
>>>>>>
>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
>>>>>> ams at login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s
>>>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a
>>>>>>
>>>>>> cd /lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>>>>
>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>>>> -DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.2/snos/lib64/libgfortran.a;/opt/gcc/4.9.2/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.2/snos/lib64/libgomp.a;/opt/gcc/4.9.2/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
>>>>>> -DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
>>>>>> -DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
>>>>>> -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/new/gromacs/gromacs-5.0.4/build
>>>>>> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a
>>>>>> -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a
>>>>>> -DCMAKE_SKIP_RPATH=ON
>>>>>>
>>>>>>
>>>>>> make
>>>>>> make install
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Oct 22, 2015 at 12:27 PM, Ana Marija <
>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>
>>>>>>> Thanks everybody for all your help!
>>>>>>>
>>>>>>> On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham <
>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija <
>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> I just tried to install it with:
>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>>>>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>>>>>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>>>>>>>>> -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>> -DGMX_X11=OFF
>>>>>>>>>
>>>>>>>>> but the error is the same as above.
>>>>>>>>>
>>>>>>>>
>>>>>>>> It can't be if you've done it properly. Use a new, empty build
>>>>>>>> directory.
>>>>>>>>
>>>>>>>>
>>>>>>>>> My goal with this installation (without cross compiler) was to use
>>>>>>>>> it to generate input files and than use another installation of gromacs
>>>>>>>>> compiled with cross compilers to complete the run. Where I would use the
>>>>>>>>> same version of gromacs in both cases, 4.6.7. Can you please confirm me
>>>>>>>>> that this is acceptable approach?
>>>>>>>>>
>>>>>>>>
>>>>>>>> Yes, but needlessly complex. You can run grompp anywhere, copy the
>>>>>>>> file to the Cray, and use the resulting .tpr on the compute nodes, like I
>>>>>>>> said a while ago.
>>>>>>>>
>>>>>>>>
>>>>>>>>> The reason why I can't use newer version of gromacs is that I only
>>>>>>>>> have cmake 2.8.4 on this machine and it is impossible to install newer
>>>>>>>>> version of cmake because it is tied to gnu version we got from Cray etc.
>>>>>>>>>
>>>>>>>>
>>>>>>>> Perhaps Cray supplied a cmake, but it doesn't run on the compute
>>>>>>>> nodes, and has nothing at all to do with the back end compilers, and your
>>>>>>>> system admins can and should be willing to download and install a more
>>>>>>>> recent cmake for you and everybody else :-)
>>>>>>>>
>>>>>>>> Mark
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll <
>>>>>>>>> sin.pecado at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija <
>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> I installed it via:
>>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
>>>>>>>>>>> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
>>>>>>>>>>> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
>>>>>>>>>>> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>
>>>>>>>>>>> then I was running it on login nodes via:
>>>>>>>>>>>
>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
>>>>>>>>>>> /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> but I didn't get .tpr file, and output was this:
>>>>>>>>>>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>>>>>>>>>>> Generated 1081 of the 1081 non-bonded parameter combinations
>>>>>>>>>>> Generating 1-4 interactions: fudge = 0.5
>>>>>>>>>>> Generated 994 of the 1081 1-4 parameter combinations
>>>>>>>>>>>
>>>>>>>>>>> -------------------------------------------------------
>>>>>>>>>>> Program grompp, VERSION 4.6.7
>>>>>>>>>>> Source code file:
>>>>>>>>>>> /lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803
>>>>>>>>>>>
>>>>>>>>>>> Fatal error:
>>>>>>>>>>> [ file tip3p.itp, line 39 ]:
>>>>>>>>>>> Atom index (1) in settles out of bounds (1-0).
>>>>>>>>>>> This probably means that you have inserted topology section
>>>>>>>>>>> "settles"
>>>>>>>>>>> in a part belonging to a different molecule than you intended to.
>>>>>>>>>>> In that case move the "settles" section to the right molecule.
>>>>>>>>>>>
>>>>>>>>>>> can you please advise what should I do in this situation?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> As Justin said, this isn't an issue with the GROMACS build
>>>>>>>>>> anymore (but rather with the inputs). So it seems that the original problem
>>>>>>>>>> is solved - unless you really need to run grompp on the compute nodes.
>>>>>>>>>>
>>>>>>>>>> BTW, I hope you know that 4.6.7 is a rather old and outdated
>>>>>>>>>> version; the 5.0 and 5.1 series has been released since and the former is
>>>>>>>>>> AFAIK supported by PLUMED!
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> --
>>>>>>>>>> Szilárd
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <
>>>>>>>>>>> sokovic.anamarija at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> so is it ok to try this?
>>>>>>>>>>>> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/
>>>>>>>>>>>> 3.3.4.0/abudhabi/include -DFFTWF_LIBRARY=/opt/fftw/
>>>>>>>>>>>> 3.3.4.0/abudhabi/lib/libfftw3f.a -DCMAKE_CXX_COMPILER=g++
>>>>>>>>>>>> -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON
>>>>>>>>>>>> -DGMX_GPU=OFF -DGMX_MPI=OFF
>>>>>>>>>>>> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
>>>>>>>>>>>> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <
>>>>>>>>>>>> mark.j.abraham at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Your blas and lapack were compiled with gfortran, but in a way
>>>>>>>>>>>>> that they require that one links further dependencies to use them later on.
>>>>>>>>>>>>> So compile them better, or use dynamic linking.
>>>>>>>>>>>>>
>>>>>>>>>>>>> But 99.9% of GROMACS users do not need to get involved with
>>>>>>>>>>>>> this, so just leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS
>>>>>>>>>>>>> will use its internal versions.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Mark
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>
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