You will have to recompile everything: make clean make You still have references to lam in your libmd_mpi.so
Roland On Tue, Mar 3, 2009 at 3:03 PM, Manik Mayur <manik.ma...@gmail.com> wrote: > > > 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.- Show quoted text - > > > 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 >> > - Show quoted text - > > > > -- > 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
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