AMBER Archive (2006)

Subject: RE: AMBER: amber9 compilation error on SGI altix

From: Lihua Wang (lhw_at_broyde.nyu.edu)
Date: Sat Apr 22 2006 - 17:48:40 CDT

Hi Ross,

Thanks for your reply. I tried your suggestion by changing the CPLUSPLUS
value.

This time the serial compilation was completed successfully but the test
failed at:

cd pb_pgb; ./Run.pbpgb
getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
   ./Run.pbpgb: Program error

And here is the stderr:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander 40000000000B00A1 Unknown Unknown
Unknown
sander 4000000000099980 Unknown Unknown
Unknown
sander 40000000000917F0 Unknown Unknown
Unknown
sander 40000000005EDB50 Unknown Unknown
Unknown
sander 40000000001D1600 Unknown Unknown
Unknown
sander 40000000001807B0 Unknown Unknown
Unknown
sander 400000000017EFF0 Unknown Unknown
Unknown
sander 4000000000003E50 Unknown Unknown
Unknown
libc.so.6.1 2000000001AF6970 Unknown Unknown
Unknown
sander 4000000000003840 Unknown Unknown
Unknown
make: *** [test.sander.BASIC] Error 1

> To: amber_at_scripps.edu
> Subject: RE: AMBER: amber9 compilation error on SGI altix
>
> Dear Lihua,
>
>> ifort -o nucgen nucgen.o ngfil.o ../lib/amopen.o ../lib/mexit.o
>> ../lib/nxtsec.o -lscs
>> icpc -c -o elsize.o elsize.cc
>>
>> /usr/include/c++/3.2.3/limits(1894): error: expected a ")"
>> { return __glibcpp_long_double_signaling_NaN; }
>> ^
>
>
> Anyway, edit $AMBERHOME/src/config.h
>
> and change
>
> CPLUSPLUS = icpc
>
> to
>
> CPLUSPLUS = icpc -cxxlib-icc
>
> Then try recompiling. Note if things still don't work you can edit
> $AMBERHOME/src/etc/Makefile and remove the elsize$(SFX) entry from the list
> of progs. elsize is a small standalone program that you only need for
> finding a molecule's size when running igb>0 and alpb=1.
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu