Hello AMBER developers,
I made a simulation system containing protein and copper ions using the CHARMM-GUI server. I used the ff19SB and Lipid17 force fields and the 12-6-4 parameters to make the system topology file. The water model was TIP3P, and the salt concentration was 0.15 M. When I run the system on the CPU version, it seems fine, but when I try to run it on the GPU version, I get the following segfault error:
"
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x2b21126ec3ff in ???
#1 0x62cd3c in ???
#2 0x4b8009 in ???
#3 0x51bd67 in ???
#4 0x4f919d in ???
#5 0x44ca1c in ???
#6 0x2b21126d8554 in ???
#7 0x45c23d in ???
#8 0xffffffffffffffff in ???
/var/lib/slurmd/job63704945/slurm_script: line 18: 47392 Segmentation fault (core dumped) pmemd.cuda -O -i step5_production.mdin -p step3_input.parm7 -c step4.5_equilibration.rst7 -o prod_1.mdout -r prod_1.rst7 -inf prod_1.mdinfo -ref step3_input.rst7 -x prod_1.nc
"
Plus, when I make a system without the 12-6-4 parameters, the system keeps running without error. There has to be something wrong with the 12-6-4 parameters and the GPU version of the software. All the input files can be found here:
https://urldefense.com/v3/__https://www.dropbox.com/s/yaqyqtsdwesgqhr/protein.tar?dl=0__;!!HXCxUKc!z2Y-DFhqFfBLBz9FrVPrp8l10posRKGttfKBLpV14znHX5yzLUx-W_xF2LGRFtmHR4F0btBf-76PJEDdNXXcmnA$
I used the gcc-10.2.0 and nvcc-11.1.1 compilers; the GPU card was NVIDIA-A100.
I would be grateful if you could help me with this.
Best regards,
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Received on Thu Oct 20 2022 - 12:00:03 PDT
