Error allocating array natoms_this_frag
- ryangmullen
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7 years 10 months ago - 7 years 10 months ago #149
by ryangmullen
hmmm...even with your files, I don't get an error allocating natoms_this_frag for either intel-compiled or gfortran-compiled Cassandra. Can you try running Cassandra with a smaller fragment library, just to see if it is a memory-related issue? By default the library_setup.py script will generate a fragment library with 100,000 configurations. You can change that using the -n flag:
> library_setup.py CASSANDRA_DIR/Src/cassandra.exe mixture.inp ipa.pdb water.pdb -n 100
where CASSANDRA_DIR is the path to your Cassandra executable, and the "-n 100" tells the script to write 100 fragment conformations instead of 100,000.
P.S. I did have to change a few keywords in your input file to get it to run:
prop_Freq ----> prop_freq
coord_Freq ----> coord_freq
remove "# Done_Simulation_Length_Info"
energy_Total ----> energy_total
> library_setup.py CASSANDRA_DIR/Src/cassandra.exe mixture.inp ipa.pdb water.pdb -n 100
where CASSANDRA_DIR is the path to your Cassandra executable, and the "-n 100" tells the script to write 100 fragment conformations instead of 100,000.
P.S. I did have to change a few keywords in your input file to get it to run:
prop_Freq ----> prop_freq
coord_Freq ----> coord_freq
remove "# Done_Simulation_Length_Info"
energy_Total ----> energy_total
Last Edit: 7 years 10 months ago by ryangmullen.
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7 years 10 months ago #150
by andy900301
Hello.
I thought it was some problem with my computer. But I changed to use another one, which gave me some details about the failure. It reflected errors like this.
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7F108ECEC777
#1 0x7F108ECECD7E
#2 0x7F108E428D3F
#3 0x453D72 in __input_routines_MOD_get_fragment_coords
#4 0x4717E5 in __input_routines_MOD_get_molecule_info
#5 0x4F0CAA in gcmc_control_
#6 0x402EA5 in MAIN__ at main.f90:?
Segmentation fault (core dumped)
I thought it was some problem with my computer. But I changed to use another one, which gave me some details about the failure. It reflected errors like this.
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7F108ECEC777
#1 0x7F108ECECD7E
#2 0x7F108E428D3F
#3 0x453D72 in __input_routines_MOD_get_fragment_coords
#4 0x4717E5 in __input_routines_MOD_get_molecule_info
#5 0x4F0CAA in gcmc_control_
#6 0x402EA5 in MAIN__ at main.f90:?
Segmentation fault (core dumped)
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