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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