Hi,
You say that you're using gcc-4.8.1 and openmpi-1.6.5 on CentOS 5.1. I
guess that it is a non-standard implementation and that you installed
gcc and openmpi "manually".
How did you install openmpi? Using the configure_openmpi script in
$AMBERHOME/AmberTools/src?
Did you try compiling Amber14 with the default gcc version in CentOS
5.1? I don't have access to CentOS 5.1, but I have a machine running
CentOS 5.7 and the default gcc version is 4.1.2...
Gerald.
On 06/15/2014 08:26 AM, 余青芬 wrote:
> Dear AMBER community,
>
>
>
> I have recently made the serial and parallel tests of Amber14 using gcc-4.8.1 and openmpi-1.6.5 on CentOS 5.1, there are some errors in running sebomd and qmmm2 test:
>
>
>
>
>
> (1) The sebomd/MNDO/dimethylether test fails for me in serial, the test hangs forever on the min.csh and md.csh script. And I add in the namelist “screen=2,” for both min.in and md.in, and the outputs min_yu.out and md_yu.out are attached in sebomd_MNDO_dimethylether_serial_yu file.
>
>
>
>
>
> (2) The sebomd/DC/water32 test has errors in parallel (2, 4 and 8 processes):
>
>
>
> cd sebomd/DC/water32 && ./min.csh && ./md.csh
>
> ERROR IN DOFERM -- NO CONVERGENCE IN FERMI ENERGY DETERMINATION
>
> ERROR IN DOFERM -- NO CONVERGENCE IN FERMI ENERGY DETERMINATION
>
> ERROR IN DOFERM -- NO CONVERGENCE IN FERMI ENERGY DETERMINATION
>
> ERROR IN DOFERM -- NO CONVERGENCE IN FERMI ENERGY DETERMINATION
>
> --------------------------------------------------------------------------
>
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 1.
>
>
>
> And I also add in the namelist “screen=2,” for both min.in and md.in, and the outputs min_yu.out and md_yu.out are attached in sebomd_DC_water32_parallel_yu file.
>
>
>
>
>
> (3) The qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0 test in parallel (8 processes) has the following error:
>
>
>
> cd qmmm2/xcrd_build_test/ && ./Run.ortho_qmewald0
>
> * NB pairs 145 185645 exceeds capacity ( 185750) 3
>
> SIZE OF NONBOND LIST = 185750
>
> SANDER BOMB in subroutine nonbond_list
>
> Non bond list overflow!
>
> check MAXPR in locmem.f
>
> --------------------------------------------------------------------------
>
> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with errorcode 1.
>
>
>
> And the qmmm2/xcrd_build_test/ && ./Run.truncoct_qmewald0 test in parallel (8 processes) has the similar error.
>
>
>
>
>
> (4) The qmmm2/adqmmm_h2o-box && ./Run.adqmmm-fixedR-calc_wbk2 in parallel (8 processes) has the following error:
>
>
>
> export TESTsander=/home/yuqingfen/software/amber14/bin/sander.MPI && cd qmmm2/adqmmm_h2o-box && ./Run.adqmmm-fixedR-calc_wbk2
>
> Running multisander version of sander Amber14
>
> Total processors = 8
>
> Number of groups = 4
>
> --------------------------------------------------------------------------
>
> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD with errorcode 1.
>
>
>
>
>
> Thank you for your help and look forward to your soon reply.
>
>
>
>
>
> --
> Qingfen Yu
> Center for High Performance Computing
> Shenzhen Institutes of Advanced Technology
> Chinese Academy of Sciences
> 1068 Xueyuan Avenue, Shenzhen University Town
> Shenzhen, P.R. China, 518055
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Sun Jun 15 2014 - 00:30:02 PDT
