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.anamar...@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.abra...@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.anamar...@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.anamar...@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.anamar...@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@login1:/lustre/beagle2/ams/lib2>ln -s >>>>> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a >>>>> ams@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@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@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@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.anamar...@gmail.com> wrote: >>>>> >>>>>> Thanks everybody for all your help! >>>>>> >>>>>> On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham < >>>>>> mark.j.abra...@gmail.com> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> On Thu, Oct 22, 2015 at 6:58 PM Ana Marija < >>>>>>> sokovic.anamar...@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.pec...@gmail.com> wrote: >>>>>>>> >>>>>>>>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija < >>>>>>>>> sokovic.anamar...@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.anamar...@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.abra...@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 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>> >>>>> >>>> >>> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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