On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz <rol...@utk.edu> wrote:
> you will have to set > > LD_LIBRARY_PATH to /home/openmpi/lib > I have tried that.. the error still persists. use either setenv or export depending on your shell > > Roland > > On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur <manik.ma...@gmail.com> wrote: > >> this time upon executing : >> ./configure\ >> --prefix /home/local/gromacs\ >> --enable-mpi\ >> --program-suffix="_mpi"\ >> --disable-nice\ >> --enable-shared\ >> MPICC=/home/openmpi/mpicc\ >> >> it exited with the following error: >> >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rw' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to >> `lam_deregister_object' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_register_objects' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to >> `sfh_sock_accept_tmout' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to >> `sfh_sock_open_srv_inet_stm' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to >> `sfh_sock_set_buf_size' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to >> `sfh_sock_open_clt_inet_stm' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `kpause' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect' >> ../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrstore' >> collect2: ld returned 1 exit status >> make[1]: *** [mdrun] Error 1 >> >> what is the problem now? >> - Show quoted text - >> >> >> On Wed, Mar 4, 2009 at 12:43 AM, Manik Mayur <manik.ma...@gmail.com>wrote: >> >>> >>> >>> On Wed, Mar 4, 2009 at 12:28 AM, Nicolas <nsa...@ucalgary.ca> wrote: >>> >>>> Manik Mayur a écrit : >>>> >>>>> >>>>> >>>>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsa...@ucalgary.ca <mailto: >>>>> nsa...@ucalgary.ca>> wrote: >>>>> >>>>> Manik Mayur a écrit : >>>>> >>>>> Hi, >>>>> >>>>> If I have 2 mpi environments, namely LAM and openMPI, and I >>>>> want gromacs to use openMPI of the two, what extra option >>>>> should I pass during the ./configure step? In my case openMPI >>>>> is installed locally(in my /home folder). >>>>> >>>>> Sorry, I've misunderstood your message. Anyway, I would first >>>>> check twice the paths to the binaries in my script. Then, I would >>>>> check my environment variables, especially PATH, LD_LIBRARY_PATH >>>>> and LD_RUN_PATH. You might need to modify them to make sure any >>>>> Lam-related stuff is loaded by default in your environment. >>>>> >>>>> >>>>> ok, is there any specific option or environment variable through which >>>>> I can make gromacs aware of openMPI and not LAM while installation? If I >>>>> carry on the default --enable-mpi thing, upon executing the following: >>>>> >>>> Just a silly question: Did you recompile Gromacs with openMPI? If not, >>>> you should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you >>>> should have something like: >>>> >>>> ./configure\ >>>> --prefix /home/local/gromacs\ >>>> --enable-mpi\ >>>> --program-suffix="_mpi"\ >>>> --without-x\ >>>> --disable-nice\ >>>> MPICC=/path/to/mpicc\ >>> >>> >>> thanks, I think that is what I needed. Let me try and then I will let you >>> know. >>> >>> >>>> CC=/path/to/gcc >>>> CPPFLAGS=-I/path/to/fftw/include/\ >>>> LDFLAGS=-L/path/to/fftw/lib/ >>>> >>> >>> Why is FFTW necessary? In all my gromacs installations till now, I have >>> avoided this package (out of ignorance). >>> >>> >>> >>>> mpicc is located in the bin/ directory of openMPI. gcc is the regular >>>> gcc installation (gcc 3). As I said, your issue is probably due to a path >>>> uncorrectly pointing to Lam. So check/modify your environment variables, >>>> especially the paths to loaded libraries. >>>> >>>> >>>>> $/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o >>>>> eql_mpi.trr >>>>> >>>>> I get the following error: >>>>> >>>>> ------------------------------------------------ >>>>> It seems that there is no lamd running on this host, which >>>>> indicates >>>>> that the LAM/MPI runtime environment is not operating. The >>>>> LAM/MPI >>>>> runtime environment is necessary for MPI programs to run (the MPI >>>>> program tired to invoke the "MPI_Init" function). >>>>> >>>>> Please run the "lamboot" command the start the LAM/MPI runtime >>>>> environment. See the LAM/MPI documentation for how to invoke >>>>> "lamboot" across multiple machines. >>>>> >>>>> >>>>> ----------------------------------------------------------------------------- >>>>> so it is like mdrun_mpi was configured with LAM and hence it is looking >>>>> for it. >>>>> >>>>> I've tried to use a local installation of openMPI myself, but >>>>> finally asked my sysadmin to install it for all users. I had many >>>>> problems with libraries that couldn't be loaded properly. >>>>> >>>>> Cheers, >>>>> Nicolas >>>>> >>>>> >>>>> Thanks, >>>>> Manik >>>>> >>>>> >>>>> On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <nsa...@ucalgary.ca >>>>> <mailto:nsa...@ucalgary.ca> <mailto:nsa...@ucalgary.ca >>>>> >>>>> <mailto:nsa...@ucalgary.ca>>> wrote: >>>>> >>>>> Hi, >>>>> >>>>> As mentioned by the error message: >>>>> >>>>> >>>>> Please run the "lamboot" command the start the LAM/MPI >>>>> runtime >>>>> >>>>> Before using Lam, you have to boot it. In my scripts, I've >>>>> got >>>>> something like: >>>>> >>>>> lamboot -v $PBS_NODEFILE >>>>> lamrun -v -np $NPROC mdrun mdargs >>>>> lamhalt >>>>> >>>>> I don't use Lam often, though, you might need to use >>>>> different Lam >>>>> options. >>>>> >>>>> Nicolas >>>>> >>>>> Manik Mayur a écrit : >>>>> >>>>> Hi, >>>>> >>>>> I have till now successfully used openMPI and gromacs >>>>> together. Recently I got a cluster where I tried to >>>>> install >>>>> openMPI and gromacs locally as I donot have root >>>>> priviledges >>>>> on it. But it turns out that it already has MPI >>>>> environment on >>>>> it (LAM) which I donot want to use (as the version is >>>>> quite >>>>> old.. the cluster still has gcc-3.2.3!). >>>>> So after installing openMPI 1.3 and gromacs 4.0.4 on it >>>>> (in my >>>>> /home folder), I tried to execute: >>>>> >>>>> $/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s >>>>> eql_mpi.tpr -o >>>>> eql_mpi.trr >>>>> >>>>> It gives the following error: >>>>> >>>>> >>>>> ----------------------------------------------------------------------------- >>>>> It seems that there is no lamd running on this host, >>>>> which >>>>> indicates >>>>> that the LAM/MPI runtime environment is not operating. >>>>> The >>>>> LAM/MPI >>>>> runtime environment is necessary for MPI programs to >>>>> run (the MPI >>>>> program tired to invoke the "MPI_Init" function). >>>>> >>>>> Please run the "lamboot" command the start the LAM/MPI >>>>> runtime >>>>> environment. See the LAM/MPI documentation for how to >>>>> invoke >>>>> "lamboot" across multiple machines. >>>>> >>>>> ----------------------------------------------------------------------------- >>>>> >>>>> My question is - Why it still tries to look for LAM >>>>> environment or lamd? I will be extremely thankful if >>>>> somebody >>>>> gives a hint. >>>>> >>>>> -Manik >>>>> -- Graduate student >>>>> Microfluidics Lab >>>>> Dept. of Mechanical Engg. >>>>> IIT Kharagpur >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org> >>>>> <mailto:gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org>> >>>>> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at >>>>> http://www.gromacs.org/search >>>>> before posting! >>>>> Please don't post (un)subscribe requests to the list. >>>>> Use the >>>>> www interface or send it to >>>>> gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org> >>>>> <mailto:gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org>>. >>>>> >>>>> Can't post? Read >>>>> http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org> >>>>> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >>>>> >> >>>>> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search >>>>> before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org> >>>>> <mailto:gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org>>. >>>>> >>>>> Can't post? Read >>>>> http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> >>>>> -- Graduate student >>>>> Microfluidics Lab >>>>> Dept. of Mechanical Engg. >>>>> IIT Kharagpur >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search >>>>> before posting! >>>>> Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org>. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> <mailto:gmx-users@gromacs.org> >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the >>>>> www interface or send it to gmx-users-requ...@gromacs.org >>>>> <mailto:gmx-users-requ...@gromacs.org>. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Graduate student >>>>> Microfluidics Lab >>>>> Dept. of Mechanical Engg. >>>>> IIT Kharagpur >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> _______________________________________________ >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>>> Please search the archive at http://www.gromacs.org/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use the www >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>> >>>> >>>> _______________________________________________ >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://www.gromacs.org/mailman/listinfo/gmx-users >>>> Please search the archive at http://www.gromacs.org/search before >>>> posting! >>>> Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> >>> >>> -- >>> Graduate student >>> Microfluidics Lab >>> Dept. of Mechanical Engg. >>> IIT Kharagpur >>> >> >> >> >> -- >> Graduate student >> Microfluidics Lab >> Dept. of Mechanical Engg. >> IIT Kharagpur >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
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