Hi, Scott
I found this problem, these files are not updated to executable. It is
weird because in the patch the files are updated to 755 mode. I will check
and maybe
another patch is needed to correct this bug.
The files in master branch are good to use. If you want to test you can
copy the directory test/nfe in master branch to your amber16 directory.
This should work.
Best regards
Feng
On Fri, Jul 29, 2016 at 4:41 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> Hi,
>
> Feng, I saw your commit fixing this, but i have not tested it yet.
>
> Another thing that needs to be fixed in the Amber16 update is these
> permissions:
> Jul 29 4:34:14pm haswell1.ten 232$ /usr/local/amber/amber16/test/nfe ll
> 4 -rw-r--r-- 1 530 Jul 27 03:18 run-parallel.sh
> 4 -rw-r--r-- 1 506 Jul 27 03:18 run-pmemd-parallel.sh
> 4 -rw-r--r-- 1 447 Jul 27 03:18 run-pmemd-serial.sh
> 4 -rw-r--r-- 1 454 Jul 27 03:18 run-serial.sh
>
> cd nfe && ./run-serial.sh
> /bin/sh: ./run-serial.sh: Permission denied
> make[2]: [test.nfe.serial] Error 126 (ignored)
>
> scott
>
> On Wed, Jul 27, 2016 at 07:51:27PM -0400, Feng Pan wrote:
> > Hi, Scott
> >
> > Thanks for the check and I got the issue. I will rewrite the amflsh to
> > close/reopen codes.
> >
> > Best
> > Feng
> >
> > On Wed, Jul 27, 2016 at 4:34 PM, Scott Brozell <sbrozell.rci.rutgers.edu
> >
> > wrote:
> >
> > > Hi,
> > >
> > > I just committed a workaround for building pmemd.mic_native which
> > > affects other pmemd executables.
> > > The recent nfe commits in the master as well as update 4 for Amber 16
> > > have broken the build for this and probably pmemd.mic_offload and
> > > pmemd.mic_native.MPI as well although i have not checked for the latter
> > > two.
> > >
> > > Detailed comments are in commit
> e672566f293a810f34a708dd67e0ed854089999f
> > > Here's the gist:
> > > the call to amflsh was commented out;
> > > amflsh should be permanently replaced with close/reopen per comments in
> > > various pmemd source files.
> > >
>
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>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Fri Jul 29 2016 - 17:30:02 PDT
