On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz <rol...@utk.edu> wrote:
> You will have to recompile everything: > make clean > make > I tried that but to no avail, then I tried building static libs by removing --enable-shared in ./configure and it got compiled and installed properly. Thanks to all, as for now, its working to my need. But somehow still I feel that with openmpi-1.3, gromacs-4.0.4 and Xeon Quad core at 3.6Ghz, the processing speed which I am getting, is quite low. 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 > > _______________________________________________ > 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
_______________________________________________ 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
