AMBER Archive (2009)

Subject: [AMBER] logdvdl does not work

From: helde010_at_umn.edu
Date: Tue Sep 08 2009 - 11:53:14 CDT

Hello AMBER listserv,

I am doing thermodynamic integration calculations and I would like to use
the logdvdl option described in the AMBER 10 manual on page 106. However,
whenever I set it equal to 1 to try to turn it on, AMBER segfaults.

For this listserv post I tried to make a reproducible error, so I used the
input files from Tutorial A6. I used the input files for the implicit
solvent calculation part of the tutorial, taking the example for
model_step2.mdin and changing ntx to 1 and irest to 0. In the groupfile
model_step2.group I changed the starting coordinate file to the one
provided in the first section of the tutorial.

The calculation runs fine with only those changes. But when I add the line
logdvdl=1 to the input file I get a segfault. Here is the output:

 Running multisander version of sander amber10
    Total processors = 2
    Number of groups = 2
 
[blade286:01527] *** Process received signal *** [blade286:01528] ***
Process received signal *** [blade286:01528] Signal: Segmentation fault
(11) [blade286:01528] Signal code: Address not mapped (1) [blade286:01528]
Failing at address: 0x8 [blade286:01527] Signal: Segmentation fault (11)
[blade286:01527] Signal code: Address not mapped (1) [blade286:01527]
Failing at address: 0x8 [blade286:01527] [ 0] /lib64/tls/libpthread.so.0
[0x2a961d2720] [blade286:01527] [ 1]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(softcore_mp_log_dvdl_+0x38)
[0x691580] [blade286:01527] [ 2]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(mix_frcti_+0x71d) [0x5fc41d]
[blade286:01527] [ 3] /usr/local/amber/amber10-OMPI/exe/sander.MPI
[0x53832b] [blade286:01527] [ 4]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(sander_+0x7187) [0x4ea56f]
[blade286:01527] [ 5]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(MAIN__+0x1382) [0x4e3352]
[blade286:01527] [ 6]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(main+0x32) [0x43f5fa]
[blade286:01528] [ 0] /lib64/tls/libpthread.so.0 [0x2a961d2720]
[blade286:01528] [ 1]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(softcore_mp_log_dvdl_+0x38)
[0x691580] [blade286:01528] [ 2]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(mix_frcti_+0x71d) [0x5fc41d]
[blade286:01528] [ 3] /usr/local/amber/amber10-OMPI/exe/sander.MPI
[0x53835c] [blade286:01528] [ 4]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(sander_+0x7187) [0x4ea56f]
[blade286:01528] [ 5]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(MAIN__+0x1382) [0x4e3352]
[blade286:01528] [ 6]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(main+0x32) [0x43f5fa]
[blade286:01528] [ 7] /lib64/tls/libc.so.6(__libc_start_main+0xea)
[0x2a962f8aaa] [blade286:01528] [ 8]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(free+0x4a) [0x43f52a]
[blade286:01528] *** End of error message *** [blade286:01527] [ 7]
/lib64/tls/libc.so.6(__libc_start_main+0xea) [0x2a962f8aaa]
[blade286:01527] [ 8]
/usr/local/amber/amber10-OMPI/exe/sander.MPI(free+0x4a) [0x43f52a]
[blade286:01527] *** End of error message *** mpirun noticed that job rank
0 with PID 1527 on node blade286 exited on signal 11 (Segmentation fault).
1 additional process aborted (not shown)

[1]+ Exit 139 mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile
model_step1.group

I did not compile this executable, it was compiled by a sysadmin of the
system I am running this on. It is AMBER 10 and I know they compiled with
open MPI. Is there a way I can make this work? For the sake of statistics
it would be nice to have all the dvdl values, without having to print a
huge output file.

-Hugh Heldenbrand
Graduate Student, University of Minnesota

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber