[QE-users] Error while running Quantum Espresso with Intel MPI
Nicola Marzari
nicola.marzari at epfl.ch
Thu Feb 14 00:47:38 CET 2019
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nicola
On 13/02/2019 17:16, Will DeBenedetti wrote:
> HI David,
>
> Have you attempted to compile with MPICH or OpenMPI? If so, can you
> provide the output files after running an example calculation?
>
> Thanks,
>
>> On Feb 13, 2019, at 5:11 PM, DAVID BARCENE <david.barcene at utp.ac.pa
>> <mailto:david.barcene at utp.ac.pa>> wrote:
>>
>>
>> Hello, I'm new to quantum espresso and I'm having some issues while
>> running the examples. I installed QE in my laptop (Lenovo Thinkpad
>> E480, i7-8550U running Fedora 29) using intel mpi to take advantage of
>> the quad core cpu. I have compiled QE using the intel fortran compiler
>> and intel C compiler including the MKL provided by the Intel Paralell
>> Studio XE 2019 update 1 cluster edition. No warnings or errors were
>> shown during the compilation but when I run the example
>> ~/qe-6.3/PW/examples/example01 it just aborts. A forum suggested to
>> set FI_LOG_LEVEL= debug to collect logs and this is the output I get:
>>
>> ********************************************************************************************************************************************
>> [dbarcene at NGC2501 example01]$ ./run_example
>>
>> /home/dbarcene/qe-6.3/PW/examples/example01 : starting
>>
>> This example shows how to use pw.x to calculate the total energy and
>> the band structure of four simple systems: Si, Al, Cu, Ni.
>>
>> executables directory: /home/dbarcene/qe-6.3/bin
>> pseudo directory: /home/dbarcene/qe-6.3/pseudo
>> temporary directory: /home/dbarcene/qe-6.3/tempdir
>> checking that needed directories and files exist... done
>>
>> running pw.x as: mpirun -np 4 /home/dbarcene/qe-6.3/bin/pw.x -nk 1
>> -nd 1 -nb 1 -nt 1
>>
>> running the scf calculation for Si...Abort(1094543) on node 1 (rank 1
>> in comm 0): Fatal error in PMPI_Init: Other MPI error, error stack:
>> MPIR_Init_thread(639)......:
>> MPID_Init(860).............:
>> MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed
>> (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
>> Abort(1094543) on node 2 (rank 2 in comm 0): Fatal error in PMPI_Init:
>> Other MPI error, error stack:
>> MPIR_Init_thread(639)......:
>> MPID_Init(860).............:
>> MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed
>> (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
>> Abort(1094543) on node 3 (rank 3 in comm 0): Fatal error in PMPI_Init:
>> Other MPI error, error stack:
>> MPIR_Init_thread(639)......:
>> MPID_Init(860).............:
>> MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed
>> (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
>> Abort(1094543) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init:
>> Other MPI error, error stack:
>> MPIR_Init_thread(639)......:
>> MPID_Init(860).............:
>> MPIDI_NM_mpi_init_hook(689): OFI addrinfo() failed
>> (ofi_init.h:689:MPIDI_NM_mpi_init_hook:No data available)
>> [cli_1]: readline failed
>> forrtl: error (78): process killed (SIGTERM)
>> Image PC Routine Line
>> Source
>> pw.x 0000000001A5EAC4 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007FE6FEB3B030 Unknown Unknown
>> Unknown
>> pw.x 00000000011BF2F0 Unknown Unknown
>> Unknown
>> pw.x 0000000000CBA309 Unknown Unknown
>> Unknown
>> pw.x 0000000000CB9D37 Unknown Unknown
>> Unknown
>> pw.x 0000000000407286 Unknown Unknown
>> Unknown
>> pw.x 0000000000407222 Unknown Unknown
>> Unknown
>> libc-2.28.so 00007FE6FADC0413 __libc_start_main Unknown
>> Unknown
>> pw.x 000000000040712E Unknown Unknown
>> Unknown
>> forrtl: error (78): process killed (SIGTERM)
>> Image PC Routine Line
>> Source
>> pw.x 0000000001A5EAC4 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F05A7AEF030 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F05A7AEDDC0 __read Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F05A65D399F Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F05A65D2D32 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F05A4C158D0 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F05A4CC6613 MPIR_Err_return_c Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F05A58AA299 MPI_Init Unknown
>> Unknown
>> libmpifort.so.12. 00007F05A40114EB MPI_INIT Unknown
>> Unknown
>> pw.x 0000000000CBA2F8 Unknown Unknown
>> Unknown
>> pw.x 0000000000CB9D37 Unknown Unknown
>> Unknown
>> pw.x 0000000000407286 Unknown Unknown
>> Unknown
>> pw.x 0000000000407222 Unknown Unknown
>> Unknown
>> libc-2.28.so 00007F05A3D74413 __libc_start_main Unknown
>> Unknown
>> pw.x 000000000040712E Unknown Unknown
>> Unknown
>> forrtl: error (78): process killed (SIGTERM)
>> Image PC Routine Line
>> Source
>> pw.x 0000000001A5EAC4 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F73A282A030 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F73A2828DC0 __read Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F73A130E99F Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F73A130DD32 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F739F9508D0 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F739FA01613 MPIR_Err_return_c Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F73A05E5299 MPI_Init Unknown
>> Unknown
>> libmpifort.so.12. 00007F739ED4C4EB MPI_INIT Unknown
>> Unknown
>> pw.x 0000000000CBA2F8 Unknown Unknown
>> Unknown
>> pw.x 0000000000CB9D37 Unknown Unknown
>> Unknown
>> pw.x 0000000000407286 Unknown Unknown
>> Unknown
>> pw.x 0000000000407222 Unknown Unknown
>> Unknown
>> libc-2.28.so 00007F739EAAF413 __libc_start_main Unknown
>> Unknown
>> pw.x 000000000040712E Unknown Unknown
>> Unknown
>> forrtl: error (78): process killed (SIGTERM)
>> Image PC Routine Line
>> Source
>> pw.x 0000000001A5EAC4 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F114000F030 Unknown Unknown
>> Unknown
>> libpthread-2.28.s 00007F114000DDC0 __read Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F113EAF399F Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F113EAF2D32 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F113D1358D0 Unknown Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F113D1E6613 MPIR_Err_return_c Unknown
>> Unknown
>> libmpi.so.12.0.0 00007F113DDCA299 MPI_Init Unknown
>> Unknown
>> libmpifort.so.12. 00007F113C5314EB MPI_INIT Unknown
>> Unknown
>> pw.x 0000000000CBA2F8 Unknown Unknown
>> Unknown
>> pw.x 0000000000CB9D37 Unknown Unknown
>> Unknown
>> pw.x 0000000000407286 Unknown Unknown
>> Unknown
>> pw.x 0000000000407222 Unknown Unknown
>> Unknown
>> libc-2.28.so 00007F113C294413 __libc_start_main Unknown
>> Unknown
>> pw.x 000000000040712E Unknown Unknown
>> Unknown
>> Error condition encountered during test: exit status = 179
>> Aborting
>> ***************************************************************************************************************************************
>>
>> Thanks in advance for any help you may provide.
>> All the best
>> David Barcene
>>
>>
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>
> William DeBenedetti
> Cornell University
>
>
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--
----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL
Director, National Centre for Competence in Research NCCR MARVEL, EPFL
http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project
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