[gmx-users] Problem configuring openMPI
Manik Mayur
manik.mayur at gmail.com
Tue Mar 3 20:35:30 CET 2009
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?
On Wed, Mar 4, 2009 at 12:43 AM, Manik Mayur <manik.mayur at gmail.com> wrote:
>
>
> On Wed, Mar 4, 2009 at 12:28 AM, Nicolas <nsapay at ucalgary.ca> wrote:
>
>> Manik Mayur a écrit :
>>
>>>
>>>
>>> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsapay at ucalgary.ca <mailto:
>>> nsapay at 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 <nsapay at ucalgary.ca
>>> <mailto:nsapay at ucalgary.ca> <mailto:nsapay at ucalgary.ca
>>>
>>> <mailto:nsapay at 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 at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> <mailto:gmx-users at gromacs.org
>>> <mailto:gmx-users at 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-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>
>>> <mailto:gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>>.
>>>
>>> Can't post? Read
>>> http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at 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-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>
>>> <mailto:gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at 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 at gromacs.org
>>> <mailto:gmx-users at 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-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at 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-request at gromacs.org
>>> <mailto:gmx-users-request at 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 at 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-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list gmx-users at 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-request at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090304/6f0bdffd/attachment.html>
More information about the gromacs.org_gmx-users
mailing list