Compile NAMD on MIPS cpu(Loongson 2F)

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Fri Sep 05 2008 - 23:23:38 CDT

Dear all,
         I am trying to compile NAMD2.6 on a MIPS cpu cluster. The
compiling process seems to go through without fatal error information.
         The problem is in run time. When I try to run NAMD in parallel
mode, it aborted with the following error message:

         Info: NAMD 2.6 for Linux-i686-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for mpi-linux
Info: Built Sat Sep 6 11:42:32 CST 2008 by BiocompASU on node1410
Info: 1 NAMD 2.6 Linux-i686-MPI 12 node2812 BiocompASU
Info: Running on 12 processors.
Info: 7328 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to /home/users/BiocompASU/test
Info: Configuration file is runmd.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: VELOCITY FILE generate.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME ouput/generate.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: XST FILENAME ouput/generate.xst
Info: XST FREQUENCY 5000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME ouput/generate
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ouput/generate.restart
Info: RESTART FREQUENCY 10000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 12
Info: SWITCHING OFF 14
Info: PAIRLIST DISTANCE 16
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 18.5
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 275
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1220673929
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB generate.pdb
Info: STRUCTURE FILE generate.psf
Info: PARAMETER file: XPLOR format! (default)
Info: PARAMETERS parameter.elements
Info: PARAMETERS param19x.pro
Info: PARAMETERS param19.rcv
Info: PARAMETERS param19.sol
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES generate.coor
Info: SUMMARY OF PARAMETERS:
Info: 94 BONDS
Info: 255 ANGLES
Info: 68 DIHEDRAL
Info: 76 IMPROPER
Info: 0 CROSSTERM
Info: 37 VDW
Info: 3 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 6694 ATOMS
Info: 6724 BONDS
Info: 9238 ANGLES
Info: 3444 DIHEDRALS
Info: 3313 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 20082 DEGREES OF FREEDOM
Info: 5393 HYDROGEN GROUPS
Info: TOTAL MASS = 76380.2 amu
Info: TOTAL CHARGE = -2.99999 e
Info: *****************************
Info: Entering startup phase 0 with 7328 kB of memory in use.
Info: Entering startup phase 1 with 7328 kB of memory in use.
Info: Entering startup phase 2 with 7328 kB of memory in use.
Info: Entering startup phase 3 with 7328 kB of memory in use.
Info: PATCH GRID IS 4 BY 4 BY 2
Info: REMOVING COM VELOCITY -0.0992981 0.0529856 0.0742762
Info: LARGEST PATCH (21) HAS 559 ATOMS
Info: CREATING 525 COMPUTE OBJECTS
Info: Entering startup phase 4 with 7328 kB of memory in use.
Info: Entering startup phase 5 with 7328 kB of memory in use.
Info: Entering startup phase 6 with 7328 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 7328 kB of memory in use.
Info: CREATING 525 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 2.71051e-20 AT 14.2807
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 9.46264e-14 AT 13.9261
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.97047e-22 AT 13.9261
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.70792e-15 AT 13.9261
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 4.93038e-32 AT 13.7818
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 2.75256e-14 AT 13.9261
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 3.08149e-33 AT 13.9261
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.25762e-15 AT 13.9261
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.65436e-24 AT 14.2105
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.80645e-15 AT 13.9261
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 9.69352e-27 AT 13.9261
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.26168e-16 AT 13.9261
Info: Entering startup phase 8 with 7328 kB of memory in use.
Info: Finished startup with 7328 kB of memory in use.
rank 2 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 2: killed by signal 11
rank 5 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 5: killed by signal 11
rank 6 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 6: killed by signal 11
rank 10 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 10: killed by signal 11
rank 11 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 11: killed by signal 11
rank 9 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 9: killed by signal 11
  exit status of rank 9: killed by signal 11
rank 4 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 4: killed by signal 11
rank 3 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 3: killed by signal 11
rank 7 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 7: killed by signal 11
rank 8 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 8: killed by signal 11
rank 1 in job 2 node2812_48675 caused collective abort of all ranks
  exit status of rank 1: killed by signal 11

-
I googled the web, and some posting said that it is related to the compiler.
the compiler I used was gcc 4.1.2, together with MPICH2 version 1.06.

Thanks for any help!

Zhi Guo

-- 
Guo Zhi

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