[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Mark Abraham mark.j.abraham at gmail.com
Fri Oct 23 20:45:10 CEST 2015 

Hi,

On Fri, Oct 23, 2015 at 7:52 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> after cmake step I got this:
> CMake Warning:
>   Manually-specified variables were not used by the project:
>
>     BUILD_SHARED_EXE
>

This doesn't exist, don't use it.


>     GMX_BUILD_SHARED_EXE
>

This doesn't exist in 5.0.4, because we added it after then. That's awkward
because PLUMED only claims to support 5.0.4. Probably later 5.0.x are fine
if one was to make a frankenstein, but since PLUMED 2.2 supports 5.1, use
that.


>     GMX_FORCE_CXX
>

This was only present in GROMACS 4.6, as it is no longer useful in 5.x.


>     MPI_LIBRARY
>

This is not useful at all - that's what cray's MPI wrapper compilers are
for.

Mark


> 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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