From: Arvind Kannan (arvind_at_caltech.edu)
Date: Fri Aug 19 2011 - 17:31:06 CDT
I'm having trouble getting the CUDA version of NAMD to run on my lab's cluster. In particular, despite adding the path to the libcudart.so.2 file in the environment variable LD_LIBRARY_PATH, namd is still unable to locate the file. Calling env tells me that
The user's guide suggests that the problem might be that charmrun does not preserve the value of LD_LIBRARY_PATH when run without the ++local option. However, the variable remains unchanged after trying to run charmrun, so that doesn't seem to be the case. Additionally, the other shared libraries that namd finds successfully don't seem to come from the directories in the library pathfile:
libdl.so.2 => /lib64/libdl.so.2 (0x000000312b400000)
libcudart.so.2 => not found
libm.so.6 => /lib64/libm.so.6 (0x000000312bc00000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x000000312c400000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x000000312d000000)
libc.so.6 => /lib64/libc.so.6 (0x000000312b000000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x000000312b800000)
I tried the user's guide's suggestion of putting
in a runscript, and running charmun with the ++runscript option, but it didn't help. LD_LIBRARY_PATH is unchanged by the runscript when run by charmun, even though the script works fine when sourced from the command line.
Any suggestions would be greatly appreciated.
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