Hi Ross,
I tried with the individual run as you suggested and got the follows:
bash-4.1$ ./Run_md_trpcage -1 SPDP
./Run_md_trpcage: Program error
bash-4.1$
The trpcage_md.out file contains the following:
| PMEMD implementation of SANDER, Release 11
| Run on 04/03/2012 at 10:22:55
[-O]verwriting output
File Assignments:
| MDIN: mdin
| MDOUT: trpcage_md.out
| INPCRD: inpcrd
| PARM: prmtop
| RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
Here is the input file:
TRPCage MD
&cntrl
imin=0, irest=1, ntx=5,
nstlim=20, dt=0.002,
ntc=2, ntf=2,
ntt=1, tautp=0.5,
tempi=325.0, temp0=325.0,
ntpr=1, ntwx=0,ntwr=100000,
ntb=0, igb=1,
cut=9999.,rgbmax=9999.
/
-------------Thus there is no output produced. In case you may want to
know, the devicequery for CUDA device produces:
bash-4.1$ ../../../../../../NVIDIA_GPU_Computing_SDK/C/bin/linux/release/deviceQuery
[../../../../../../NVIDIA_GPU_Computing_SDK/C/bin/linux/release/deviceQuery]
starting...
../../../../../../NVIDIA_GPU_Computing_SDK/C/bin/linux/release/deviceQuery
Starting...
CUDA Device Query (Runtime API) version (CUDART static linking)
There are 2 devices supporting CUDA
Device 0: "Tesla M2090"
CUDA Driver Version / Runtime Version 4.10 / 4.10
CUDA Capability Major/Minor version number: 2.0
Total amount of global memory: 5375 MBytes (5636554752 bytes)
( 0) Multiprocessors x (32) CUDA Cores/MP: 0 CUDA Cores
GPU Clock Speed: 1.30 GHz
Memory Clock rate: 1848.00 Mhz
Memory Bus Width: 384-bit
L2 Cache Size: 786432 bytes
Max Texture Dimension Size (x,y,z) 1D=(1), 2D=(0,65536),
3D=(134217728,65536,65535)
Max Layered Texture Size (dim) x layers 1D=(65000) x 65000,
2D=(1048544,16384) x 16384
Total amount of constant memory: 65536 bytes
Total amount of shared memory per block: 49152 bytes
Total number of registers available per block: 32768
Warp size: 32
Maximum number of threads per block: 1024
Maximum sizes of each dimension of a block: 1024 x 1024 x 64
Maximum sizes of each dimension of a grid: 65535 x 65535 x 65535
Maximum memory pitch: 2147483647 bytes
Texture alignment: 512 bytes
Concurrent copy and execution: Yes with 2048 copy engine(s)
Run time limit on kernels: Yes
Integrated GPU sharing Host Memory: Yes
Support host page-locked memory mapping: No
Concurrent kernel execution: Yes
Alignment requirement for Surfaces: Yes
Device has ECC support enabled: Yes
Device is using TCC driver mode: Yes
Device supports Unified Addressing (UVA): Yes
Device PCI Bus ID / PCI location ID: 2048 / 16384
Compute Mode:
< Default (multiple host threads can use ::cudaSetDevice() with
device simultaneously) >
Device 1: "GeForce 8400 GS"
CUDA Driver Version / Runtime Version 4.10 / 4.10
CUDA Capability Major/Minor version number: 1.1
Total amount of global memory: 511 MBytes (536150016 bytes)
( 0) Multiprocessors x ( 8) CUDA Cores/MP: 0 CUDA Cores
GPU Clock Speed: 1.40 GHz
Memory Clock rate: 333.00 Mhz
Memory Bus Width: 64-bit
Max Texture Dimension Size (x,y,z) 1D=(1), 2D=(0,8192),
3D=(134217728,65536,32768)
Max Layered Texture Size (dim) x layers 1D=(65000) x 65000,
2D=(1048544,0) x 0
Total amount of constant memory: 65536 bytes
Total amount of shared memory per block: 16384 bytes
Total number of registers available per block: 8192
Warp size: 32
Maximum number of threads per block: 512
Maximum sizes of each dimension of a block: 512 x 512 x 64
Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
Maximum memory pitch: 2147483647 bytes
Texture alignment: 256 bytes
Concurrent copy and execution: Yes with 512 copy engine(s)
Run time limit on kernels: No
Integrated GPU sharing Host Memory: Yes
Support host page-locked memory mapping: No
Concurrent kernel execution: Yes
Alignment requirement for Surfaces: Yes
Device has ECC support enabled: Yes
Device is using TCC driver mode: Yes
Device supports Unified Addressing (UVA): No
Device PCI Bus ID / PCI location ID: 512 / 8192
Compute Mode:
< Default (multiple host threads can use ::cudaSetDevice() with
device simultaneously) >
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4.10, CUDA
Runtime Version = 4.10, NumDevs = 2, Device = Tesla M2090, Device =
GeForce 8400 GS
[../../../../../../NVIDIA_GPU_Computing_SDK/C/bin/linux/release/deviceQuery]
test results...
PASSED
Press ENTER to exit...
Thanks
> Hi Mohammad,
>
> Do you get any other errors than just 'program error'?
>
> Could you try running one of the tests manually?
>
> cd $AMBERHOME/test/cuda/trpcage/
> ./Run_md_trpcage -1 SPDP
>
> Then post the messages you get to the screen and also the contents of
> trpcage_md.out
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Mohammad Ashraf Bhuiyan [mailto:akasheee.gmail.com]
>> Sent: Monday, April 02, 2012 5:44 PM
>> To: amber.ambermd.org
>> Subject: [AMBER] Amber GPU test fails
>>
>> Hi,
>> I installed Amber cpu version and works fine.
>>
>> Then i tried GPU version. I applied latest bugfixes for Ambertools 1.5
>> and Amber11. The Amber11 is also installed for cuda without any
>> errors. But when I tried with the test,
>> ./test_amber_cuda.sh, then it throws error, such as:
>>
>> bash-4.1$ ./test_amber_cuda.sh
>> Using default GPU_ID = -1
>> Using default PREC_MODEL = SPDP
>> cd cuda && make -k test.pmemd.cuda GPU_ID=-1 PREC_MODEL=SPDP
>> make[1]: Entering directory
>> `/localdisk/ashraf/Amber/amber11_cuda/amber11/test/cuda'
>> ------------------------------------
>> Running CUDA Implicit solvent tests.
>> Precision Model = SPDP
>> GPU_ID = -1
>> ------------------------------------
>> cd trpcage/ && ./Run_md_trpcage -1 SPDP netcdf.mod
>> ./Run_md_trpcage: Program error
>> make[1]: *** [test.pmemd.cuda.gb] Error 1
>> cd gb_ala3/ && ./Run.igb1_ntc1_min -1 SPDP netcdf.mod
>> ./Run.igb1_ntc1_min: Program error
>> make[1]: *** [test.pmemd.cuda.gb.serial] Error 1
>> ------------------------------------
>> Running CUDA Explicit solvent tests.
>> Precision Model = SPDP
>> GPU_ID = -1
>> ------------------------------------
>> cd 4096wat/ && ./Run.pure_wat -1 SPDP netcdf.mod
>> ./Run.pure_wat: Program error
>> make[1]: *** [test.pmemd.cuda.pme] Error 1
>> make[1]: Target `test.pmemd.cuda' not remade because of errors.
>> make[1]: Leaving directory
>> `/localdisk/ashraf/Amber/amber11_cuda/amber11/test/cuda'
>> make: *** [test.pmemd.cuda] Error 2
>>
>>
>>
>> Also I tried to run benchmark listed, such as DHFR NVE = 23,558 atoms
>> given in the Amber website. It does not produce any output. It does
>> not crash. But the mdout file only has the input listed, no output.
>>
>>
>> Did anyone experience this kind of errors. Any idea will be
>> appreciated?
>> I am using Nvidia 2090 and it works fine for other CUDA code.
>>
>>
>> --
>> Best Regards
>>
>> Ashraf
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 2 Apr 2012 22:58:09 -0700 (PDT)
> From: Acoot Brett <acootbrett.yahoo.com>
> Subject: [AMBER] how where to read the amber and amber test failure
> diff files
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <1333432689.26423.YahooMailNeo.web121805.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
>
>
> Dear All,
>
> After the AMBERTOOLS test nd AMBER test, for the failure test, it suggest to read the diff file.
>
> Do all the failure test diff file exist in the final single diff file? Otherwise I could not locate the specific diff file.
>
> I am looking forward to getting a reply from you on it.
>
> Cheers,
>
> Acoot
>
> ------------------------------
>
> Message: 8
> Date: Mon, 2 Apr 2012 23:14:36 -0700 (PDT)
> From: Acoot Brett <acootbrett.yahoo.com>
> Subject: [AMBER] on "-v" in mdrun
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <1333433676.21007.YahooMailNeo.web121801.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset=utf-8
>
>
>
> Dear All,
>
> For the function of mdrun. will you please introduce the time difference for the whole mdrun with or without "-v"? I suppose with "-v" will need some calculation time, but I am not sure whether the time spent is significant.
>
> Cheers,
>
> Acoot
>
>
> ------------------------------
>
> Message: 9
> Date: Tue, 3 Apr 2012 08:50:41 +0200
> From: francesco oteri <francesco.oteri.gmail.com>
> Subject: Re: [AMBER] Use of PCASuite in analyzing DNA-MD trajectories
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAFQcp-PK_h82DVYe3S68qRB5R6JZzvok7MR2UphFv+4Aae9XnQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> perhaps your trajectory is too large.
> Try to use a smaller trajectory, with only CA for example.
>
> Francesco
>
>
> Il giorno 02 aprile 2012 20:53, Muhammad Khaled Tumbi <khaledtumbi.gmail.com
>> ha scritto:
>
>> Hi,
>> did any one used Principle Component Analysis method to analyse the
>> molecular dynamics trajectory (Meyer et al., J. Chem. Theor. Comp. 2006, 2,
>> 251-258 ).
>> I am trying this using PCASuite (pcazip) but getting error " not enough
>> memory allocating -553492920 bytes"
>> Can anybody help me to solve this problem
>> Regards
>> =-=-=-=
>> Tumbi Muhammed Khaled Abdul Waheed,
>> Institute Scholar,
>> Department Of Pharmacoinformatics,
>> NIPER, S.A.S. Nagar, Mohali,
>> Punjab, India.
>> Mob. +91 78145 24855
>> www.niper.ac.in
>> www.pharmacoinformatics.info
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
>
> ------------------------------
>
> Message: 10
> Date: Tue, 03 Apr 2012 12:01:20 +0200
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] metal site
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20120403120120.0kz1e55aw0kok8k4.webmail.u-picardie.fr>
> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> format="flowed"
>
> Dear Per,
>
> Did you follow the bonded and non-bonded energy values?
> Is there any 'problem' with the 1-4 electrostatic term for instance?
>
> regards, Francois
>
>
>> I have some problems with a metal site I have parametrized in a protein. It
>> is a copper site with four cysteine residue - so I start by doing a QM
>> optimization of the geometry and getting a charge model using the
>> Merz-Kollman in Turbomole. When I minimize with the newly added parameters
>> the equilibrium distances and angles are reached - also during heating and
>> for the first 20 ns of simulation but after 20 ns it starts to become
>> strange two of the sulfur atoms come very close (~1.8 ?) both are
>> negatively charged and stays there furthermore the equilibrium distance is
>> no longer sampled for the S-Cu distance it is shorten by 0.2 ?. The force
>> constant for the metal-sulfur interaction is around 40 so it should be
>> quite a penalty to the energy but mean and SD are the same.
>>
>> Clearly something is wrong but I have no idea how to narrow it down - I
>> have create the residues using templates from library files of e.g. CYM and
>> HIE and the generated frcmod file with the missing parameters. I have added
>> a new atom type for the sulfur but is added as atom type "S" "sp3". I have
>> check the prmtop and it contains the force constants etc. Also in the leap
>> log I do not see any errors or warnings related to the metal site and its
>> residues.
>>
>> all suggestions are more then welcome and needed
>
>
>
>
>
> ------------------------------
>
> Message: 11
> Date: Tue, 3 Apr 2012 11:27:49 +0100
> From: Dureid El-Moghraby <D.El-Moghraby.leeds.ac.uk>
> Subject: [AMBER] "Possible Failures" in Amber 11 and Amber tools tests
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <CBA07230.7E19%d.el-moghraby.leeds.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear all,
>
>
> I am currently in the process of getting Amber 11 and
> Ambertools 1.5 installed on our institution's computing cluster. Both
> Amber tools and Amber compiled with no errors.
>
> The tests for Amber 11 came back with some errors and possible failures.
> All the errors and some of the failures are those mentioned by
> AT15_Amber11.py . There are a few of the file comparison tests that failed
> and are not in the expected list of
> failed tests. In the case of Amber Tools there were about 10 failed file
> comparisons. For the parallel versions there was 1 and 7 comparison
> failure for Amber and Amber tools
> respectively.
>
> II have included the logs and diff files for these with this
> email. Unfortunately, I do not know enough to judge whether these
> differences are at an acceptable level, and given the diverse nature of
> our research community, cannot be sure that these features will not be
> used. Any help you can provide would be much appreciated.
>
>
>
> Please find the configuration details below.
>
> RHEL 5
> Intel compilers version 12.0.2
> MKL 10.3u2 and OpenMPI 1.4.
>
> Bugfix level:
> Ambertools 1.5 : fixes 1-26
> Amber 11: bugfix.all.tar.bz2 contain up to bugfix18
>
> Configuration:
> SSE_TYPES="SSE3,SSE4.2"
> ./configure intel (serial)
> ./configure -mpi intel (parallel)
>
>
>
> Kind regards,
>
> Dureid
>
>
>
>
>
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 113, Issue 1
> *************************************
--
Best Regards
Ashraf
--------------------------------------------------
M Ashraf Bhuiyan, PhD
Hillsboro, OR, USA
_______________________________________________
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AMBER.ambermd.org
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Received on Tue Apr 03 2012 - 11:00:03 PDT
