[gmx-users] Problem configuring openMPI
Roland Schulz
roland at utk.edu
Tue Mar 3 20:48:46 CET 2009
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.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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>>
>>
>>
>> --
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>>
>
>
>
> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
>
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