[gmx-users] Problem configuring openMPI
Manik Mayur
manik.mayur at gmail.com
Tue Mar 3 21:47:00 CET 2009
On Wed, Mar 4, 2009 at 1:55 AM, Roland Schulz <roland at 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.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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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -- 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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>> - 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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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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