Hi, Chunli
You should only use the pmemd.cuda.MPI to do string method since string
method requires
many images on the path.
In the error, it seems some integer is divided by zero, could you send me
the mdin file to
check if any error in inputs?
Best
Feng
On Tue, Aug 1, 2017 at 3:00 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
> 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*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Aug 01 2017 - 13:00:03 PDT
