Hi,
There have been some old posts on the message:
> Permissions not found for every file in
but without enough details to know the consequences.
Since amber 16 update 4 may be relevant to your interests, try this
update_amber --show-applied-patches
Also you can edit your files to see if the update.4 changes have been made.
That's is a first step before debugging this:
> Once I finish the installing and ran string methods with pmemd.duda. I got
scott
On Tue, Aug 01, 2017 at 03:00:33PM -0400, Chunli Yan wrote:
>
> 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
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Received on Tue Aug 01 2017 - 13:00:02 PDT
