I completed the install/testing of Amber 10 on my Ubuntu system. Thanks
Ross...
I installed the parallel version with no errors with only a single
manual modification of the config_amber.h file
using the default MPI (openmpi) for Ubuntu
>apt-get install libopenmpi-dev libopenmpi1 openmpi-bin openmpi-common
openmpi-doc
which puts all MPI includes and libraries in /usr/lib/openmpi.
so defining MPI_HOME appropriately
>export MPI_HOME=/usr/lib/openmpi
I configure the build with
> ./configure_amber -openmpi gfortran
which I then edit, config_amber.h manually because the wrapper compilers
mpicc and mpif90 are installed into /usr/bin and not $MPI_HOME/bin as
the ./configure_amber script expects
in config_amber.h:
change FC to
FC=/usr/bin/mpif90
and change LOAD
LOAD= /usr/bin/mpif90 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
then compile with
>make parallel
The build completed without errors.
So moving to the test
>cd $AMBERHOME/test
>export DO_PARALLEL="mpirun -np 4"
>make test.parallel.MM
runs through several successful tests, but eventually fails at
cd cnstph && ./Run.cnstph
[ubuntu1:28131] *** Process received signal ***
[ubuntu1:28133] *** Process received signal ***
[ubuntu1:28133] Signal: Segmentation fault (11)
[ubuntu1:28133] Signal code: Address not mapped (1)
[ubuntu1:28133] Failing at address: (nil)
[ubuntu1:28133] [ 0] [0x4001a410]
[ubuntu1:28132] *** Process received signal ***
[ubuntu1:28132] Signal: Segmentation fault (11)
[ubuntu1:28132] Signal code: Address not mapped (1)
[ubuntu1:28132] Failing at address: 0x6a7ef9db
[ubuntu1:28131] Signal: Segmentation fault (11)
[ubuntu1:28131] Signal code: Address not mapped (1)
[ubuntu1:28131] Failing at address: 0x5
[ubuntu1:28132] [ 0] [0x4001a410]
[ubuntu1:28132] [ 1]
/home/surfer/tmp/amber10/exe/sander.MPI(sander_+0x6f45) [0x80f49fd]
[ubuntu1:28132] [ 2]
/home/surfer/tmp/amber10/exe/sander.MPI(MAIN__+0x106c) [0x80eda34]
[ubuntu1:28133] [ 1]
/home/surfer/tmp/amber10/exe/sander.MPI(sander_+0x6f45) [0x80f49fd]
[ubuntu1:28132] [ 3] /home/surfer/tmp/amber10/exe/sander.MPI(main+0x39)
[0x841d3f9]
[ubuntu1:28133] [ 2]
/home/surfer/tmp/amber10/exe/sander.MPI(MAIN__+0x106c) [0x80eda34]
[ubuntu1:28132] [ 4]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe5) [0x402ce685]
[ubuntu1:28133] [ 3] /home/surfer/tmp/amber10/exe/sander.MPI(main+0x39)
[0x841d3f9]
[ubuntu1:28132] [ 5] /home/surfer/tmp/amber10/exe/sander.MPI [0x807aaa1]
[ubuntu1:28133] [ 4]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe5) [0x402ce685]
[ubuntu1:28132] *** End of error message ***
Any help on how to proceed would be appreciated.
searches of the archives for Run.cnstph returned errors that were
different from this.
Cheers,
--Jim
UTSA Physics
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Received on Sun Apr 12 2009 - 01:16:11 PDT
