you will have to set LD_LIBRARY_PATH to /home/openmpi/lib
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
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