[gmx-users] Problem configuring openMPI
Roland Schulz
roland at utk.edu
Tue Mar 3 21:25:42 CET 2009
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.mayur at gmail.com> wrote:
>
>
> On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz <roland at 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.mayur at 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.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
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>> -- 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>
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>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Graduate student
>>>>>> Microfluidics Lab
>>>>>> Dept. of Mechanical Engg.
>>>>>> IIT Kharagpur
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Graduate student
>>>> Microfluidics Lab
>>>> Dept. of Mechanical Engg.
>>>> IIT Kharagpur
>>>>
>>>
>>>
>>>
>>> --
>>> Graduate student
>>> Microfluidics Lab
>>> Dept. of Mechanical Engg.
>>> IIT Kharagpur
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
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> - Show quoted text -
>
>
>
> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
>
> _______________________________________________
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--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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