[gmx-users] Problem configuring openMPI
Manik Mayur
manik.mayur at gmail.com
Tue Mar 3 21:03:14 CET 2009
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.
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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>>>>>
>>>>>
>>>>> -- Graduate student
>>>>> Microfluidics Lab
>>>>> Dept. of Mechanical Engg.
>>>>> IIT Kharagpur
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>
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>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>
>>
>>
>>
>> --
>> 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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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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