AMBER Archive (2006)

Subject: AMBER: Amber9 serial installation -tests- severe (174): SIGSEGV, segmentation fault occurred

From: Maniopoulou, A \(Mina\) (A.Maniopoulou_at_rl.ac.uk)
Date: Thu Oct 19 2006 - 07:48:08 CDT

Hi,
I am trying to do the serial installation for amber9 for a cluster with i686 architecture and Xeon processor, running RedHat Linux 3.
I use the intel compilers 9.1038 (for icc and icpc) and ifort (9.10.32). My mkl library is version 8.1.
 
When I run the tests most of them pass, but I have problem with the following:

tets.sander.DIVCON
The Run.wnmr in the water2_qmmmnmr/ dir passes
but the Run.cnmr produces the following
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 0858BC31 Unknown Unknown Unknown
sander 0850A75D Unknown Unknown Unknown
sander 0846C80B Unknown Unknown Unknown
sander 08439AEE Unknown Unknown Unknown
sander 0841E46E Unknown Unknown Unknown
sander 08413787 Unknown Unknown Unknown
sander 08419831 Unknown Unknown Unknown
sander 08121911 Unknown Unknown Unknown
sander 0810FD60 Unknown Unknown Unknown
sander 0810C8ED Unknown Unknown Unknown
sander 0804BD3E Unknown Unknown Unknown
libc.so.6 0018579A Unknown Unknown Unknown
sander 0804BC71 Unknown Unknown Unknown
  ./Run.cnmr: Program error

The divcon.out created contains up to line 40 of the divcon.out.save, that is it includes the ADDITIONAL(DEFAULT) KEYWORDS and nothing further down.

The mdout.cmr conatins the first 146 lines of the mdout.cmr.save, that is its last lines are

   eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 46923
| TOTAL SIZE OF NONBOND LIST = 46923
.

test.antechamber produces segementation faults as well. Specifically
inthe tp/ dir the script Run.tp produces:
Running: $AMBERHOME/exe/divcon
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
divcon 083D420A Unknown Unknown Unknown
divcon 083CDA48 Unknown Unknown Unknown
divcon 083C891B Unknown Unknown Unknown
divcon 08276CDE Unknown Unknown Unknown
divcon 08209354 Unknown Unknown Unknown
divcon 0820776C Unknown Unknown Unknown
divcon 0804BBCE Unknown Unknown Unknown
libc.so.6 0015F79A Unknown Unknown Unknown
divcon 0804BB01 Unknown Unknown Unknown
Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in charge.c properly, exit

5c5
< bcc
---
> No Charge or Current Charge
7,19c7,19
< 1 CG -1.959 0.102 0.795 ca 1 TP -0.118
< 2 CD1 -1.249 0.602 -0.303 ca 1 TP -0.113
< 3 CD2 -2.071 0.865 1.963 ca 1 TP 0.016
< 4 CE1 -0.646 1.863 -0.234 ca 1 TP -0.137
< 5 C6 -1.472 2.129 2.031 ca 1 TP -0.145
< 6 CZ -0.759 2.627 0.934 ca 1 TP -0.112
< 7 HE2 -1.558 2.719 2.931 ha 1 TP 0.129
< 8 S15 -2.782 0.365 3.060 sh 1 TP -0.254
< 9 H19 -3.541 0.979 3.274 hs 1 TP 0.191
< 10 H29 -0.787 -0.043 -0.938 ha 1 TP 0.134
< 11 H30 0.373 2.045 -0.784 ha 1 TP 0.133
< 12 H31 -0.092 3.578 0.781 ha 1 TP 0.133
< 13 H32 -2.379 -0.916 0.901 ha 1 TP 0.143
---
> 1 CG -1.959 0.102 0.795 ca 1 TP 0.
> 2 CD1 -1.249 0.602 -0.303 ca 1 TP 0.
> 3 CD2 -2.071 0.865 1.963 ca 1 TP 0.
> 4 CE1 -0.646 1.863 -0.234 ca 1 TP 0.
> 5 C6 -1.472 2.129 2.031 ca 1 TP 0.
> 6 CZ -0.759 2.627 0.934 ca 1 TP 0.
> 7 HE2 -1.558 2.719 2.931 ha 1 TP 0.
> 8 S15 -2.782 0.365 3.060 sh 1 TP 0.
> 9 H19 -3.541 0.979 3.274 hs 1 TP 0.
> 10 H29 -0.787 -0.043 -0.938 ha 1 TP 0.
> 11 H30 0.373 2.045 -0.784 ha 1 TP 0.
> 12 H31 -0.092 3.578 0.781 ha 1 TP 0.
> 13 H32 -2.379 -0.916 0.901 ha 1 TP 0.

No frcmod.diff produced

divcon.out contains the first 70 lines of the divcon.out.save and then blank

Same problems with the
Run.ash
Rum.sustiva
Run.fluorescein
Run.guanine

If I notice correctly, except for the first one, all the others seem to have trouble with the method bcc.

PS: I build the config.h by running ./configure -nopar -bintraj -p4 ifort_ia32 and then replace manually gcc -m32 with icc and g++ with icpc.

Thanks a lot,

Mina Maniopoulou
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