dear samir,
with openmpi relion runs fine on your ubuntu version.
please check if you do not have multiple mpi versions on your system e.g.
sudo dpkg -l | grep -i mpi
i never tried mpich here but it should work as follows:
sudo apt-get install libmpich2-dev
and then compile with
sudo MPICXX="/usr/bin/mpicxx.mpich2 -DMPICH_IGNORE_CXX_SEEK "
./INSTALL.sh -j 8
cheers,
wolfgang
On 05/09/2014 09:04 AM, Sjors Scheres wrote:
> Dear Samir,
> Make sure that relion was compiled with the same MPI installation (mpich?)
> as the one you are using to run it with. This sounds trivial, but on many
> systems it is not. For example, imagic (and other programmes) may come
> with their own MPI and "hijack" your system installed one. Commands like
> "which mpirun" in the shell where you execute relion should help.
> HTH,
> S
>
>> Hi Scheres,
>> Thanks for replay, I download relion again, after rebooting the computer.
>> I got less errors than before. I run the gui, so far ctf and extracting
>> particles worked fine. However I got this error while doing 2d
>> classification:
>>
>> Here is the command that I run:
>>
>> Executing: mpirun -n 8 `which relion_refine_mpi` --o Class2D/run1 --i
>> ./particles.star --particle_diameter 350 --angpix 1.45 --iter 25
>> --tau2_fudge 2 --flatten_solvent --K 10 --oversampling 1 --psi_step 10
>> --offset_range 30 --offset_step 2 --norm --scal
>>
>> And here is the error :
>>
>> Executing: mpirun -n 8 `which relion_refine_mpi` --o Class2D/run1 --i
>> ./particles.star --particle_diameter 350 --angpix 1.45 --iter 25
>> --tau2_fudge 2 --flatten_solvent --K 10 --oversampling 1 --psi_step 10
>> --offset_range 10 --offset_step 2 --norm --scale --j 1 &
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> /home/sb/Programs/relion-1.2/bin/relion_refine_mpi: symbol lookup error:
>> /usr/lib/libmpich.so.3: undefined symbol: MPL_env2str
>> --------------------------------------------------------------------------
>> mpirun noticed that the job aborted, but has no info as to the process
>> that caused that situation.
>>
>> Any help will be appreciated.
>> Thank you
>> Cheers,
>> Samir
>>
>
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
Institut für Struktur und Systembiologie
@ Institute of Molecular Biotechnology (IMBA)
Dr. Bohr-Gasse 3-7, Room 6.14
1030 Vienna, Austria
Tel.: +43 (1) 790 44-4649
Email: [log in to unmask]
http://www.cssb-hamburg.de/
--
DANKE FÜR 125 JAHRE ENGAGEMENT UND VERTRAUEN.
www.uke.de/125
_____________________________________________________________________
Besuchen Sie uns auf: www.uke.de
_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Christian Gerloff (Vertreter des Vorsitzenden), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
_____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
|