Hello, so here is the RESTRT Parameter input:
[-O]verwriting output
File Assignments:
| MDIN: test_runSanderMIN.mdin
| MDOUT: test_runSanderMIN.mdout
| INPCRD: test_prmCoord.crd
| PARM: test_prmTop.prmtop
| RESTRT: test_MINCoord.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: test_runSanderMIN.mdinfo
|LOGFILE: logfile
Additionally I should mention, that the test_MINCoord.rst will be written, but it is empty and the Coordinates appear in the fort.16 file instead.
A command like: mv fort.16 test_MINCoord.rst does the trick in the meanwhile.
Again, I'll observe this only for the AMBER11 CPU and GPU version, as well for the AMBER 12 GPU version, AMBER12 on CPU works fine.
This behavior is new to me since we've applied the latest patches, bevor everything was as expected.
So with that, it should state, that a file system error is not likely.
Plus, to answer the question for the compilation of input for pmemd.cuda, here is the input:
cd $AMBERHOME
./configure -cuda gnu
make -j 6 install
Thanks again for your support
Marko
------------------------------
Message: 24
Date: Tue, 5 Feb 2013 09:20:50 -0700
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] AMBER pmemd and pmemd.cuda, not restart files
after minimization - fort.16 file instead
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CAAC0qOY1gcrJ9GZH8_3ieF34n87bhFF+Z1CeW1u=3d-G3mFTxA.mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
Unfortunately I haven't been able to reproduce your behavior using any
version of the code. This may seem a silly question, but in your
output file does it look like RESTRT is being set correctly?
...
| PARM: Ala10.99SB.t3pOct.parm7
| RESTRT: ala10.rst7
| REFC: refc
...
In the pmemd code the restart file is always opened before it is
written to, yet the fort.16 file suggests that somehow the open call
is failing. As far as I can tell that means either the pmemd binary is
messed up in some way, or there are filesystem issues. All I can
suggest is to compile again starting from clean source code.
-Dan
On Tue, Feb 5, 2013 at 4:07 AM, Marko Wehle <Marko.Wehle.mpikg.mpg.de> wrote:
>
> Dear Dan and Ross,
> the input looks like the following:
>
> For pmemd on CPU
>
> full system minimization
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 1,
> ntr = 0,
> ntp = 0,
> ntf = 1,
> ntc = 1,
> cut = 10.0
> /
>
> For pmemd on GPU
>
> full system minimization
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 10000,
> ntb = 1,
> ntr = 0,
> ntp = 0,
> ntf = 1,
> ntc = 1,
> cut = 10.0
> /
>
> ncyc is here 10000, because the minimization does not work further otherwise.
>
> Command line Options:
>
> PROGRAM="pmemd.MPI"
> #run minimization...
> PROGRAM_OPTIONS="-O -i "$name"_runSanderMIN.mdin -o "$name"_runSanderMIN.mdout -p "$name"_prmTop.prmtop -c "$name"_prmCoord.crd -r "$name"_MINCoord.rst -inf "$name"_runSanderMIN.mdinfo"
> mpirun -v -d -x LD_LIBRARY_PATH -x PATH `which ${PROGRAM}` ${PROGRAM_OPTIONS}
>
>
>
>
> The requested informations, by Ross, are:
>
> AMBER11 GPU:
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 2.3
> |
> | 12/14/2011
> |
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> | Duncan Poole (nVIDIA)
> |
> | CAUTION: The CUDA code is currently experimental.
> | You use it at your own risk. Be sure to
> | check ALL results carefully.
> |
> | Precision model in use:
> | [SPDP] - Hybrid Single/Double Precision (Default).
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA Capable Devices Detected: 1
> | CUDA Device ID in use: 0
> | CUDA Device Name: Tesla M2050
> | CUDA Device Global Mem Size: 2687 MB
> | CUDA Device Num Multiprocessors: 14
> | CUDA Device Core Freq: 1.15 GHz
> |
> |--------------------------------------------------------
>
>
> and AMBER12 GPU:
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 12.2
> |
> | 01/10/2013
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> | Duncan Poole (nVIDIA)
> |
> | CAUTION: The CUDA code is currently experimental.
> | You use it at your own risk. Be sure to
> | check ALL results carefully.
> |
> | Precision model in use:
> | [SPFP] - Mixed Single/Double/Fixed Point Precision.
> | (Default)
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA Capable Devices Detected: 1
> | CUDA Device ID in use: 0
> | CUDA Device Name: Tesla M2050
> | CUDA Device Global Mem Size: 2687 MB
> | CUDA Device Num Multiprocessors: 14
> | CUDA Device Core Freq: 1.15 GHz
> |
> |--------------------------------------------------------
>
>
> Unfortunately, those kind of informations are not available for the CPU Versions of AMBER11 and AMBER12.
>
>
> Thank you a lot for your support.
> Sincerely yours,
> Marko
>
>
>
>>
>>Dear Amber Developers and Users,
>>unfortunatly I've did not get any better behavior of Amber12 pmemd.cuda
>>after minimzation steps.
>>Here a list of working steps, to let you know what our protocol for
>>installation is:
>>
>>###########################################
>>
>>tar xvfj Amber12.tar.bz2
>>tar xvfj AmberTools12.tar.bz2
>>
>>cd $AMBERHOME
>>./patch_amber.py --update-tree
>>./patch_amber.py --update-tree
>>./patch_amber.py --update-tree
>>
>># ./patch_amber.py --patch-level
>>> Latest patch applied to AmberTools12: 33
>>> Latest patch applied to Amber12: 14
>>
>>cd $AMBERHOME
>>./configure gnu
>>make -j 10 install
>>
>>#############################################
>>
>>Like described in the AMBER Bugfix section of the AMBER website, we have
>>to run the patch script several times.
>>Sincerely yours,
>>Marko
>>
>>
>>-----Urspr?ngliche Nachricht-----
>>Von: Marko Wehle
>>Gesendet: Mi 30.01.2013 21:14
>>An: amber.ambermd.org
>>Betreff: Re: AMBER pmemd and pmemd.cuda, not restart files after
>>minimization - fort.16 file instead
>>>
>>> Hello Amber Developers and Users,
>>> I'm experiencing a behavior of the AMBER11 pmemd and pmemd.cuda version,
>>> as well in AMBER12 pmemd.cuda, that is new to me.
>>> They write out an empty restart file after minimization and put the
>>>actual
>>> coordinates in an fort.16 called file.
>>> Simulations do fine.
>>> After a search on the web I found the following entry:
>>>
>>> http://archive.ambermd.org/201207/0216.html
>>>
>>> that exactly describes this behavior.
>>> The suggestion for solving the problem was recompiling AMBER11 with all
>>> patches applied.
>>> Unfortunately I could not find any further comments regarding this
>>>issue.
>>>
>>
>>bugfix.23 for Amber 11 and bugfix.7 for Amber 12 should fix this issue...
>> You can use ./patch_amber.py --patch-level in Amber 12 to see which
>>patches have been applied.
>>
>>
>>> But what is irritating here, we've got this particular problem only
>>>after
>>> we applied all the patches while recompiling AMBER11 and AMBER12 last
>>>week.
>>> It concerns the pmemd.cuda in AMBER12 only, but in AMBER11 both pmemd
>>>and
>>> pmemd.cuda.
>>> Before recompiling I did not observe this issues. The compile routine
>>>and
>>> the installation routine went fine so far and no errors were reported.
>>>
>>
>>bugfix.1 for Amber 12 and bugfix.22 for Amber 11 actually introduced this
>>issue, but I haven't seen them occur since the previous patches I
>>mentioned
>>were released.
>>
>>A temporary workaround is, of course, to use the fort.16 file instead (but
>>that won't work particularly well in an automated workflow).
>>
>>Good luck,
>>Jason
>>
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
------------------------------
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Received on Wed Feb 06 2013 - 04:00:02 PST
