AMBER Archive (2009)

Subject: [AMBER] problem running pmemd gbrna tests

From: wong105_at_llnl.gov
Date: Tue Sep 15 2009 - 13:07:14 CDT

Dear Sirs;

     I was able to successfully compile pmemd (amber 10) on a cluster
of AMD opteron processors. ifort (10.0.023) compiled the executable
and the MKL libraries were employed. The mvapich-inte-gen2-0.0.9
libraries were used.

However, I get the following error when I run the pmemd tests
(./Run.gbrna: Program error)

*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x0000000000791000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x0000000000791000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x0000000000791000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x00000000007cd000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x00000000007cd000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x00000000007c3000 ***
*** glibc detected ***
/g/g10/swong/usr/amber10/test/gb_rna/../../exe/pmemd: free(): invalid
next size (normal): 0x00000000007cd000 ***
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgcc_s.so.1 00002AAAAC871776 Unknown Unknown Unknown
libgcc_s.so.1 00002AAAAC8718A4 Unknown Unknown Unknown
libc.so.6 00002AAAAC5F7338 Unknown Unknown Unknown
libc.so.6 00002AAAAC57C80F Unknown Unknown Unknown
libc.so.6 00002AAAAC583CE2 Unknown Unknown Unknown
libc.so.6 00002AAAAC58790C Unknown Unknown Unknown
libmlx4-rdmav2.so 00002AAAAD6AB2AF Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB3BD52 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB188B5 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABAF70F4 Unknown Unknown Unknown
libfmpich.so.1.0 00002AAAAB89F11E Unknown Unknown Unknown
pmemd 00000000004AB2A6 Unknown Unknown Unknown
pmemd 00000000004B3C4E Unknown Unknown Unknown
pmemd 0000000000403BEC Unknown Unknown Unknown

Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgcc_s.so.1 00002AAAAC871776 Unknown Unknown Unknown
libgcc_s.so.1 00002AAAAC8718A4 Unknown Unknown Unknown
libc.so.6 00002AAAAC5F7338 Unknown Unknown Unknown
libc.so.6 00002AAAAC57C80F Unknown Unknown Unknown
libc.so.6 00002AAAAC583CE2 Unknown Unknown Unknown
libc.so.6 00002AAAAC58790C Unknown Unknown Unknown
libmlx4-rdmav2.so 00002AAAAD6AB2AF Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB3BD52 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB188B5 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABAF70F4libfmpich.so.1.0 00002AAAAB89F11E
  Unknown Unknown Unknown
pmemd 00000000004AB2A6 Unknown Unknown Unknown
pmemd 00000000004B3C4E Unknown Unknown Unknown
pmemd 0000000000403BEC Unknown Unknown Unknown

Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libgcc_s.so.1 00002AAAAC871776 Unknown Unknown Unknown
libgcc_s.so.1 00002AAAAC8718A4 Unknown Unknown Unknown
libc.so.6 00002AAAAC5F7338 Unknown Unknown Unknown
libc.so.6 00002AAAAC57C80F Unknown Unknown Unknown
libc.so.6 00002AAAAC583CE2 Unknown Unknown Unknown
libc.so.6 00002AAAAC58790C Unknown Unknown Unknown
libmlx4-rdmav2.so 00002AAAAD6AB2AF Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB3BD52 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABB188B5 Unknown Unknown Unknown
libmpich.so.1.0 00002AAAABAF70F4 Unknown Unknown Unknown
libfmpich.so.1.0 00002AAAAB89F11E Unknown Unknown Unknown
pmemd 00000000004AB2A6 Unknown Unknown Unknown
pmemd 00000000004B3C4E Unknown Unknown Unknown
pmemd 0000000000403BEC Unknown Unknown Unknown
   Unknown Unknown Unknown

.......

Any ideas of what may be causing this error? Fortunately, the
explicit solvent test run fine.

Thanks;

-Sergio

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