Hello,
I want to test string methods using pmemd.cuda.
Below is the steps how I compile amber16 with AmberTools16,
1. export AMBERHOME=`pwd`
2. ./update_amber --update (I can not pass update.4 and update.9 that
relate to string methods)
3. ./update_amber --apply patch=../../nfe_advance.patch/nfe_advance.patch
4. ./configure -cuda intel
5. make install
But I always have problems to pass update.4 and update.9, it complains
below:
Applying AmberTools 16/update.9.gz
/home/cyan/program/amber16/updateutils/patch.py:334: PatchingWarning:
Permissions not found for every file in
.patches/AmberTools16_Unapplied_Patches/update.9.
All new files will be read-only!
'files will be read-only!') % self.name, PatchingWarning)
Applying Amber 16/update.4.gz
/home/cyan/program/amber16/updateutils/patch.py:334: PatchingWarning:
Permissions not found for every file in
.patches/Amber16_Unapplied_Patches/update.4.
All new files will be read-only!
'files will be read-only!') % self.name, PatchingWarning)
Once I finish the installing and ran string methods with pmemd.duda. I got
the following error:
forrtl: severe (71): integer divide by zero
Image PC Routine Line Source
libintlc.so.5 00002B862BA802C9 Unknown Unknown Unknown
libintlc.so.5 00002B862BA7EB9E Unknown Unknown Unknown
libifcore.so.5 00002B862A72908F Unknown Unknown Unknown
libifcore.so.5 00002B862A690D7F Unknown Unknown Unknown
libifcore.so.5 00002B862A6A2309 Unknown Unknown Unknown
libpthread.so.0 000000397460F7E0 Unknown Unknown Unknown
pmemd.cuda 000000000071B524 Unknown Unknown Unknown
pmemd.cuda 00000000006C4EF6 Unknown Unknown Unknown
pmemd.cuda 00000000004E5CD6 Unknown Unknown Unknown
pmemd.cuda 0000000000409F66 Unknown Unknown Unknown
libc.so.6 0000003973E1ED1D Unknown Unknown Unknown
pmemd.cuda 0000000000409DE1 Unknown Unknown Unknown
[comet-34-06.sdsc.edu:mpispawn_0][child_handler] MPI process (rank: 0, pid:
186206) exited with status 71
Does anyone know what is wrong in it?
Thanks,
Best,
*Chunli*
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Received on Tue Aug 01 2017 - 12:30:02 PDT
