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Problem in parallel mode (iMPI 3.2.2)

Alexey Terent'ev
varf2@ssau.ru


Hi,
I try to get started the Firefly in the cluster in the parallel mode.
But I have a problem.

Input file BAopt.inp
! Minimize (Energy/Geometry) B3LYP
$CONTRL COORD=CART ICHARG=0 MULT=1 RUNTYP=OPTIMIZE SCFTYP=RHF $END
$DFT DFTTYP=B3LYP METHOD=GRID $END
$p2p p2p=.t. dlb=.t. xdlb=.t. $end
$BASIS DIFFSP=.true. GBASIS=N31 NGAUSS=6 POLAR=POPLE $END
$SYSTEM MEMORY=150000 $END
$DATA
6june11
C1
O 8.0 -0.0000000000 0.0000000000 0.0000000000
H 1.0 -0.8000000000 0.8000000000 0.0000000000
H 1.0 0.8000000000 0.8000000000 0.0000000000
$END

Calculation using the single process:
#!/bin/bash
#PBS -N BAopt.inp
#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:03:00
#PBS -j oe
#PBS -V
mpi_dir=/opt/intel/mpi-rt/3.2.2/bin/
cd $PBS_O_WORKDIR
PATH=$PBS_O_PATH
export I_MPI_DEVICE=rdma
export I_MPI_DEBUG=0
export I_MPI_FALLBACK_DEVICE=disable
export I_MPI_PIN_MODE=lib
export I_MPI_PIN_PROCS=0,2,1,5,3,4,6,7
mpirun -r ssh -machinefile $PBS_NODEFILE -np `cat $PBS_NODEFILE|wc -l` ./firefly -r -f -p -stdext -ex ~/ex/ -i ~/BAopt.inp -o ~/BAopt.out -t ~/tmp/

Output file BAopt.out:
Core i7 / Linux Firefly version running under Linux.
Running on Intel CPU: Brand ID 0, Family 6, Model 26, Stepping 5
CPU Brand String: Intel(R) Xeon(R) CPU X5560 @ 2.80GHz
CPU Features : CMOV, MMX, SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, HTT, MWAIT, EM64T
Data cache size: L1 32 KB, L2 256 KB, L3 8192 KB
max # of cores/package : 8
max # of threads/package : 16
max cache sharing level : 16
actual # of cores/package : 4
actual # of threads/package : 8
actual # of threads/core: 2
Operating System successfully passed SSE support test.
PARALLEL VERSION (INTEL MPI) RUNNING IN SERIAL MODE USING SINGLE PROCESS

CPU TIME: STEP = 0.00 , TOTAL = 0.2 SECONDS (0.0 MIN)
WALL CLOCK TIME: STEP = 0.00 , TOTAL = 0.2 SECONDS (0.0 MIN)
CPU UTILIZATION: STEP = 0.00%, TOTAL = 119.92%
197298 WORDS OF DYNAMIC MEMORY USED
WARNING! YOU ARE USING OUTDATED VERSION OF THE FIREFLY!
PLEASE CHECK FIREFLY HOMEPAGE FOR INFORMATION ON UPDATES!
EXECUTION OF FIREFLY TERMINATED NORMALLY 16:05:31 LT 6-JUN-2011

Calculations on two cores (Intel MPI 3.2.2 library):
#!/bin/bash
#PBS -N BAopt.inp
#PBS -l nodes=1:ppn=2
#PBS -l walltime=00:03:00
#PBS -j oe
#PBS -V
mpi_dir=/opt/intel/mpi-rt/3.2.2/bin/
cd $PBS_O_WORKDIR
PATH=$PBS_O_PATH
export I_MPI_DEVICE=rdma
export I_MPI_DEBUG=0
export I_MPI_FALLBACK_DEVICE=disable
export I_MPI_PIN_MODE=lib
export I_MPI_PIN_PROCS=0,2,1,5,3,4,6,7
mpirun -r ssh -machinefile $PBS_NODEFILE -np `cat $PBS_NODEFILE|wc -l` ./firefly -r -f -p -stdext -ex ~/ex/ -i ~/BAopt.inp -o ~/BAopt.out -t ~/tmp/

Folder /tmp/ and BAopt.dat and BAopt.out files cannot be created, in the initial file the following is written:
n122:2081: dapl_cma_active: PATH_RECORD_ERR, retries(15) exhausted, DST 172.40.103.10,2079
[0:n122] unexpected DAPL event 4008 from 1:n122
rank 0 in job 1 n122_43384 caused collective abort of all ranks
exit status of rank 0: killed by signal 9

Thank you in advance!

[ This message was edited on Mon Jun 6 '11 at 5:44pm by the author ]


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