From: Doug Stetner (d.stetner_at_imb.uq.edu.au)
Date: Tue Jul 12 2016 - 22:51:40 CDT
Hi all,
Linux 2.6.32-279.19.1.el6.x86_64 #1 SMP Wed Dec 19 07:05:20 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
openmpi/1.10.3
gcc/5.2.0
Both the current nightly build as well as the 2.11 release.
I am getting a seg fault after compiling namd2 on the test data provided:
$ ./namd2 src/alanin
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
[delta:14629] *** Process received signal ***
[delta:14629] Signal: Segmentation fault (11)
[delta:14629] Signal code: Address not mapped (1)
[delta:14629] Failing at address: (nil)
[delta:14629] [ 0] /lib64/libpthread.so.0[0x3e6a20f790]
[delta:14629] [ 1] ./namd2(_ZN11WorkDistrib30assignPatchesSpaceFillingCurveEv+0x38c)[0xb8d92c]
[delta:14629] [ 2] ./namd2(_ZN11WorkDistrib17assignNodeToPatchEv+0x43)[0xb8e013]
[delta:14629] [ 3] ./namd2(_ZN4Node7startupEv+0xb10)[0xac94c0]
[delta:14629] [ 4] ./namd2(CkDeliverMessageFree+0x22)[0xc2d132]
[delta:14629] [ 5] ./namd2(_Z15_processHandlerPvP11CkCoreState+0x10ff)[0xc331ff]
[delta:14629] [ 6] ./namd2(CsdScheduleForever+0x48)[0xce0eb8]
[delta:14629] [ 7] ./namd2(CsdScheduler+0x2d)[0xce112d]
[delta:14629] [ 8] ./namd2(_ZN9ScriptTcl3runEv+0x165)[0xb404c5]
[delta:14629] [ 9] ./namd2(_Z18after_backend_initiPPc+0x2c4)[0x612544]
[delta:14629] [10] ./namd2(main+0x1a)[0x61278a]
[delta:14629] [11] /lib64/libc.so.6(__libc_start_main+0xfd)[0x3e69e1ed5d]
[delta:14629] [12] ./namd2[0x5a8641]
[delta:14629] *** End of error message ***
Segmentation fault (core dumped)
Instrumenting the code I see that:
2210 iout << iINFO << "DGS DGS 2 " << i << endi;
(gdb) n
Info: DGS DGS 2 02211 int pe = peDiffuseOrdering[(i+1)%numNodes]; // avoid 0 if possible
(gdb) n
Program received signal SIGSEGV, Segmentation fault.
0x0000000000d7d78d in WorkDistrib::assignPatchesSpaceFillingCurve() () at src/WorkDistrib.C:2211
2211 int pe = peDiffuseOrdering[(i+1)%numNodes]; // avoid 0 if possible
peDiffuseOrdering is null
It is supposed to be initialised in
WorkDistrib::buildNodeAwarePeOrdering
which is in turn called by
static void build_ordering(void *)
Which is called by
topo_getargs(char **argv)
which is never called.
This is building with
./config Linux-x86_64-g++ --with-debug --charm-arch mpi-linux-x86_64
NAMD_2.11_Source
Anyone hit this before?
Thanks,
Douglas Stetner | Bioinformatics Systems Administrator
Division of Genomics of Development & Disease
Institute for Molecular Bioscience
Level #5 North | 306 Carmody Road (Building 80)
The University of Queensland | Brisbane QLD 4072 | Australia
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:35 CST