[gmx-users] gromacs 4.6.7 plumed -Segmentation fault
Ana Marija
sokovic.anamarija at gmail.com
Fri Oct 23 21:39:52 CEST 2015
I tried installing gromacs 5.1 and this is what I got:
ams at login1:/lustre/beagle2/ams/new/gromacs/gromacs-5.1/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-5.1/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
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc
-- Check for working C compiler: /opt/cray/craype/2.4.0/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC
-- Check for working CXX compiler: /opt/cray/craype/2.4.0/bin/CC -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Error at CMakeLists.txt:61 (message):
GROMACS cannot be installed into the build tree, choose a different
location for CMAKE_INSTALL_PREFIX
-- Configuring incomplete, errors occurred!
Can you please advise
On Fri, Oct 23, 2015 at 2:06 PM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:
> is there is anywhere installation instruction page for gromacs 5.1? like
> there is for gromacs 5.0
>
> and did any of the basic flags for cmake changed?
>
> On Fri, Oct 23, 2015 at 1:44 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>
>>>
>
More information about the gromacs.org_gmx-users
mailing list