[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Ana Marija sokovic.anamarija at gmail.com
Fri Oct 23 18:17:21 CEST 2015


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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