(unknown charset) [AMBER] sebomd and qmmm2 test failing in serial/parallel for Amber14

From: (unknown charset) 余青芬 <qf.yu.siat.ac.cn>
Date: Sun, 15 Jun 2014 14:26:54 +0800 (GMT+08:00)

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
 






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Received on Sat Jun 14 2014 - 23:30:03 PDT
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