From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Wed Sep 13 2006 - 07:06:08 CDT
Hi all,
I'm still having problems in running namd2 in our Athlon 64 Dual Core
machines. The problem is that the simulation runs well to a point where
all processes, except for one, stop, and I get a single process in a
single cpu running. The simulation does not crash, but it does not
continues as well, and this single process appears to last forever
doing something I don't know what it is.
Now, as Jim suggested, I have attached gdb to this process. I have
never used it, but I could get the information bellow. Any help is
appreciated. I believe the bolded output bellow is the one referring
to the namd2 process.
------------ OUTPUT FROM GDB: --------------------------
Attaching to program: /usr/bin/namd2, process 19438
Reading symbols from /lib64/libdl.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libm.so.6
Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols
found)...done.
Loaded symbols for /usr/lib64/libstdc++.so.6
Reading symbols from /lib64/libc.so.6...
(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols
found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols
found)...done.
Loaded symbols for /lib64/libgcc_s.so.1
Reading symbols from /lib64/libnss_files.so.2...
(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_files.so.2
0x0000000000714caa in Set::find ()
(gdb) next
Single stepping until exit from function _ZN3Set4findEP10InfoRecord,
which has no line number information.
0x00000000006f407f in Rebalancer::numAvailable ()
(gdb) next
Single stepping until exit from function
_ZN10Rebalancer12numAvailableEP11computeInfoP13processorInfoPiS4_S4_,
which has no line number information.
0x00000000006f3f34 in Rebalancer::refine_togrid ()
(gdb) next
Single stepping until exit from function
_ZN10Rebalancer13refine_togridERA3_A3_A2_NS_6pcpairEdP13processorInfoP11computeInfo,
which has no line number information.
0x00000000006f23b5 in Rebalancer::refine ()
(gdb) next
Single stepping until exit from function _ZN10Rebalancer6refineEv,
which has no line number information.
-----------------------------------------------------------------------
>From this point on nothing happens.
Thank you very much,
Leandro.
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Leandro Martinez
Institute of Chemistry
State University of Campinas, Brazil
http://www.ime.unicamp.br/~martinez/packmol
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