Re: [gmx-users] mdrun-gpu error message on Gromacs 4.5.5

[Justin Lemkul]

On 5/6/13 9:39 PM, Andrew DeYoung wrote:

Hi,

I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM).  This is my first
time using a GPU.  I get the following error message when attempting to run
mdrun-gpu with my .tpr file:

---
Program mdrun-gpu, VERSION 4.5.5
Source code file:
/usr/local/src/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line: 1365

Fatal error:
OpenMM exception caught while initializating: getPropertyValue: Illegal
property name
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I get this error when calling with:

mdrun-gpu -s topol.tpr

and with:

mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr

I can't seem to find this particular error message in the documentation or
previously discussed on this mailing list.  Does this error message suggest
that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly
installed?



It looks to be a rather generic OpenMM error message, which unfortunately isn't 
very helpful.  I got lots of those, along with random failures, that led me to 
abandon using OpenMM within Gromacs.  Support for OpenMM in Gromacs is limited 
at best, as OpenMM is being deprecated.  Is there any reason you're not using 
the native GPU support from 4.6.1?  The only reason to try to use OpenMM is for 
GPU-accelerated implicit solvent simulations, so if that's what you're doing I 
can understand.  Otherwise, use 4.6.1.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] mdrun-gpu error message on Gromacs 4.5.5

[Andrew DeYoung]

Hi,

I am running mdrun-gpu on Gromacs 4.5.5 (with OpenMM).  This is my first
time using a GPU.  I get the following error message when attempting to run
mdrun-gpu with my .tpr file: 

---
Program mdrun-gpu, VERSION 4.5.5
Source code file:
/usr/local/src/gromacs-4.5.5/src/kernel/openmm_wrapper.cpp, line: 1365

Fatal error:
OpenMM exception caught while initializating: getPropertyValue: Illegal
property name
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I get this error when calling with:

mdrun-gpu -s topol.tpr

and with:

mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no" -s topol.tpr

I can't seem to find this particular error message in the documentation or
previously discussed on this mailing list.  Does this error message suggest
that I am calling mdrun-gpu incorrectly, or that OpenMM is improperly
installed?

Thank you kindly for your time! 

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] mdrun-gpu

[Mark Abraham]

On 9/08/2012 3:47 PM, cuong nguyen wrote:

Dear Gromacs Users,

I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support.
when I run grompp-gpu to generate the .tpr file, it worked well:
grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96
however, then I run mdrun-gpu "mdrun-gpu -s min -o min -c min.g96 -x min
-e min -g min", it was stopped with the error:
Fatal error: OpenMM supports only the following integrators:
md/md-vv/md-vv-avek, sd/sd1, and bd.

Could someone please explain what this error means and the appropriate
way to remedy it?


You chose an integrator in your .mdp file, perhaps to do energy 
minimization (but since you're asking for help about a problem with your 
integrator, you should have identified which integrator you were using 
so you could tell us). It wasn't one of the legal set for GPU support. 
So you will not be able to use that integrator, and will have to use 
non-GPU GROMACS. When you are using such an integrator, you can use 
GPU-enabled GROMACS.


Mark
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[gmx-users] mdrun-gpu

[cuong nguyen]

Dear Gromacs Users,

I am trying Gromacs/4.5.5-OpenMM on GPU with CUDA support.
when I run grompp-gpu to generate the .tpr file, it worked well:
grompp-gpu -f input_min.mdp -o min.tpr -c box1.g96
however, then I run mdrun-gpu "mdrun-gpu -s min -o min -c min.g96 -x min
-e min -g min", it was stopped with the error:
Fatal error: OpenMM supports only the following integrators:
md/md-vv/md-vv-avek, sd/sd1, and bd.

Could someone please explain what this error means and the appropriate
way to remedy it?
Thank you in advance.
Best regards,

Cuong
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Re: [gmx-users] mdrun-gpu error

[Justin A. Lemkul]

   >>> --
>>> Szilárd
>>>
>>>
>>>
>>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
   mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>

>>> wrote:
>>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>>> >
>>> > Mark,
>>> >
>>> > THe normal mdrun also hangs thus not generating any
output.
>>> >
>>> >
>>> > OK. It's your problem to solve... keep simplifying stuff
   until you can
>>> > isolate a small number of possible causes. Top of the
list is
   file
>>> > system
>>> > availability.
>>> >
>>> > Mark
>>> >
>>> >
>>> >
>>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
   mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au <mailto:mark.abra...@anu.edu.au>>>

>>> > wrote:
>>> >>
>>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com>
   <mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@gmail.com>> wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> Its going into the running mode but gets hang there
for long
   hours
>>> >> which
>>> >> generating any data in the output file. And am not
able to
   figure out
>>> >> the
>>> >> error file_doc. Please anyone knows what's going wrong.
>>> >>
>>> >>
>>> >> No, but you should start trying to simplify what you're
   doing to see
>>> >> where
>>> >> the problem lies. Does normal mdrun work?
>>> >>
>>> >> Mark
>>> >>
>>> >>
>>> >> Thanks
>>> >> Sent from my BlackBerryŽ on Reliance Mobile, India's
No. 1

   Network. Go
>>> >> for
>>> >> it!
>>> >>
>>> >> -Original Message-
>>> >> From: Szilárd Páll mailto:szilard.p...@cbr.su.se>
   <mailto:szilard.p...@cbr.su.se
<mailto:szilard.p...@cbr.su.se>__>>
>>> >> Sender: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
   <mailto:gmx-users-bounces@__gromacs.org
<mailto:gmx-users-boun...@gromacs.org>>
>>> >> Date: Wed, 18 Jan 2012 14:47:59
>>> >> To: Discussion list for GROMACS
usersmailto:gmx-users@gromacs.org>
   <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>__>
>>> >> Reply-To: Discussion list for GROMACS users
   mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>__>
>>> >> Subject: Re: [gmx-users] mdrun-gpu error
>>> >>
>>> >> Hi,
>>> >>
>>> >> Most of those are just warnings, the only error I see
there
   comes from
>>> >> the shell, probably an error in your script.
>>> >>
>>> >> Cheers,
>>> >> --
>>> >> Szilárd
>>> >>
>>> >>
>>> >>
>>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>>> >> mailto:aiswarya.pa...@gmail.com>
<mailto:aiswarya.pawar@gmail.__com
<mailto:aiswarya.pa...@gmail.com>>>

   wrote:
>>> >>
>>> >> Hi users,
>>> >>
>>> &g

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

gt; availability.
>> >>> >
>> >>> > Mark
>> >>> >
>> >>> >
>> >>> >
>> >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
>>> <mailto:mark.abra...@anu.edu.**au
>> >>
>>
>> >>> > wrote:
>> >>> >>
>> >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
>><mailto:aiswarya.pawar@gmail.**com > wrote:
>>     >>> >>
>> >>> >> Hi,
>> >>> >>
>> >>> >> Its going into the running mode but gets hang there for long
>>hours
>> >>> >> which
>> >>> >> generating any data in the output file. And am not able to
>>figure out
>> >>> >> the
>> >>> >> error file_doc. Please anyone knows what's going wrong.
>> >>> >>
>> >>> >>
>> >>> >> No, but you should start trying to simplify what you're
>>doing to see
>> >>> >> where
>> >>> >> the problem lies. Does normal mdrun work?
>> >>> >>
>> >>> >> Mark
>> >>> >>
>> >>> >>
>> >>> >> Thanks
>> >>> >> Sent from my BlackBerryŽ on Reliance Mobile, India's No. 1
>>
>>Network. Go
>> >>> >> for
>> >>> >> it!
>> >>> >>
>> >>> >> -Original Message-
>> >>> >> From: Szilárd Páll ><mailto:szilard.p...@cbr.su.se**>>
>> >>> >> Sender: gmx-users-boun...@gromacs.org
>><mailto:gmx-users-bounces@**gromacs.org
>> >
>> >>> >> Date: Wed, 18 Jan 2012 14:47:59
>> >>> >> To: Discussion list for GROMACS users><mailto:gmx-users@gromacs.org>**>
>> >>> >> Reply-To: Discussion list for GROMACS users
>>mailto:gmx-users@gromacs.org>**>
>> >>> >> Subject: Re: [gmx-users] mdrun-gpu error
>> >>> >>
>> >>> >> Hi,
>> >>> >>
>> >>> >> Most of those are just warnings, the only error I see there
>>comes from
>> >>> >> the shell, probably an error in your script.
>> >>> >>
>> >>> >> Cheers,
>> >>> >> --
>> >>> >> Szilárd
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>> >>> >> > <mailto:aiswarya.pawar@gmail.**com
>> >>
>>
>>wrote:
>> >>> >>
>> >>> >> Hi users,
>> >>> >>
>> >>> >> Am running mdrun on gpu . I receive an error such as=
>> >>> >>
>> >>> >> WARNING: This run will generate roughly 38570 Mb of data
>> >>> >>
>> >>> >>
>> >>> >> WARNING: OpenMM does not support leap-frog, will use
>>velocity-verlet
>> >>> >> integrator.
>> >>> >>
>> >>> >>
>> >>> >> WARNING: OpenMM supports only Andersen thermostat with the
>> >>> >> md/md-vv/md-vv-avek integrators.
>> >>> >>
>> >>> >>
>> >>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
>> >>> >> coupling.
>> >>> >>
>> >>> >>
>> >>> >> WARNING: OpenMM provides contraints as a combination of
>>SHAKE, SETTLE
>> >>> >> and
>> >>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the
>>"shake_tol"
>> >>> >> option.
>> >>> >>
>> >>> >> /bin/cat: file_loc: No such file or directory
>> >>> >>
>> >>> >>
>> >>> >> and the job is running but the nothing written into .xtc,
>>   

Re: [gmx-users] mdrun-gpu error

[Justin A. Lemkul]

aiswarya pawar wrote:

Szilárd,

I did a memory test run yesterday and it went fine but today received an 
error. So you mean to say the tesla card version nothing to do with this 
right.




You're trying to solve multiple problems at once.  You told Mark that the normal 
mdrun executable (which works independently of any GPU components) also hangs, 
so either your filesystem is faulty or your installation procedure produced 
nonfunctional executables.


You're posting bits and pieces of information, which makes it incredibly hard 
for anyone to help you.  Let's recap and try again.  Please provide:


1. The Gromacs version you're using
2. Description of the hardware (GPU and non-GPU components)
3. Installation procedure for Gromacs and any of the prerequisite software and 
libraries that were required, including versions
4. The exact command(s) you're issuing, including the full script that is 
causing a problem


-Justin


Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll <mailto:szilard.p...@cbr.su.se>> wrote:


That's a generic GPU kernel launch failure which can mean anything,
from faulty hardware to bad driver to messed up installation.

Does the memory test run? Try to compile/install again and see if it
works.

--
Szilárd



On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
mailto:aiswarya.pa...@gmail.com>> wrote:
 > when i tired running it again, i got an error as
 >
 > Cuda error in file
 >

'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu
<http://bbsort.cu>'
 > in line 176 : unspecified launch failure.
 >
 > /bin/cat: file_loc: No such file or directory
 >
 >
 > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar
mailto:aiswarya.pa...@gmail.com>>
 > wrote:
 >>
 >> Has the tesla card got to do anything with the error. Am
using Nvidia
 >> Tesla S1070 1U server.
 >>
 >>
 >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll
mailto:szilard.p...@cbr.su.se>>
 >> wrote:
 >>>
 >>> And sorting out where the /bin/cat error comes from because that is
 >>> surely not a Gromacs message!
 >>>
 >>> Cheers,
 >>> --
 >>> Szilárd
 >>>
 >>>
 >>>
 >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
 >>> wrote:
 >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
 >>> >
 >>> > Mark,
 >>> >
 >>> > THe normal mdrun also hangs thus not generating any output.
 >>> >
 >>> >
 >>> > OK. It's your problem to solve... keep simplifying stuff
until you can
 >>> > isolate a small number of possible causes. Top of the list is
file
 >>> > system
 >>> > availability.
 >>> >
 >>> > Mark
 >>> >
 >>> >
 >>> >
 >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
 >>> > wrote:
 >>> >>
 >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com> wrote:
 >>> >>
 >>> >> Hi,
 >>> >>
 >>> >> Its going into the running mode but gets hang there for long
hours
 >>> >> which
 >>> >> generating any data in the output file. And am not able to
figure out
 >>> >> the
 >>> >> error file_doc. Please anyone knows what's going wrong.
 >>> >>
 >>> >>
 >>> >> No, but you should start trying to simplify what you're
doing to see
 >>> >> where
 >>> >> the problem lies. Does normal mdrun work?
 >>> >>
 >>> >> Mark
 >>> >>
 >>> >>
 >>> >> Thanks
 >>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1
Network. Go
 >>> >> for
 >>> >> it!
 >>> >>
 >>> >> -Original Message-
 >>> >> From: Szilárd Páll mailto:szilard.p...@cbr.su.se>>
 >>> >> Sender: gmx-users-boun...@gromacs.org
<mailto:gmx-users-boun...@gromacs.org>
 >>> >> Date: Wed, 18 Jan 2012 14:47:59
 >&g

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Szilárd,

I did a memory test run yesterday and it went fine but today received an
error. So you mean to say the tesla card version nothing to do with this
right.

Thanks

On Thu, Jan 19, 2012 at 11:09 PM, Szilárd Páll wrote:

> That's a generic GPU kernel launch failure which can mean anything,
> from faulty hardware to bad driver to messed up installation.
>
> Does the memory test run? Try to compile/install again and see if it works.
>
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
>  wrote:
> > when i tired running it again, i got an error as
> >
> > Cuda error in file
> >
> '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
> bbsort.cu'
> > in line 176 : unspecified launch failure.
> >
> > /bin/cat: file_loc: No such file or directory
> >
> >
> > On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar <
> aiswarya.pa...@gmail.com>
> > wrote:
> >>
> >> Has the tesla card got to do anything with the error. Am using Nvidia
> >> Tesla S1070 1U server.
> >>
> >>
> >> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll 
> >> wrote:
> >>>
> >>> And sorting out where the /bin/cat error comes from because that is
> >>> surely not a Gromacs message!
> >>>
> >>> Cheers,
> >>> --
> >>> Szilárd
> >>>
> >>>
> >>>
> >>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham  >
> >>> wrote:
> >>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
> >>> >
> >>> > Mark,
> >>> >
> >>> > THe normal mdrun also hangs thus not generating any output.
> >>> >
> >>> >
> >>> > OK. It's your problem to solve... keep simplifying stuff until you
> can
> >>> > isolate a small number of possible causes. Top of the list is file
> >>> > system
> >>> > availability.
> >>> >
> >>> > Mark
> >>> >
> >>> >
> >>> >
> >>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <
> mark.abra...@anu.edu.au>
> >>> > wrote:
> >>> >>
> >>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
> >>> >>
> >>> >> Hi,
> >>> >>
> >>> >> Its going into the running mode but gets hang there for long hours
> >>> >> which
> >>> >> generating any data in the output file. And am not able to figure
> out
> >>> >> the
> >>> >> error file_doc. Please anyone knows what's going wrong.
> >>> >>
> >>> >>
> >>> >> No, but you should start trying to simplify what you're doing to see
> >>> >> where
> >>> >> the problem lies. Does normal mdrun work?
> >>> >>
> >>> >> Mark
> >>> >>
> >>> >>
> >>> >> Thanks
> >>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network.
> Go
> >>> >> for
> >>> >> it!
> >>> >>
> >>> >> -Original Message-
> >>> >> From: Szilárd Páll 
> >>> >> Sender: gmx-users-boun...@gromacs.org
> >>> >> Date: Wed, 18 Jan 2012 14:47:59
> >>> >> To: Discussion list for GROMACS users
> >>> >> Reply-To: Discussion list for GROMACS users 
> >>> >> Subject: Re: [gmx-users] mdrun-gpu error
> >>> >>
> >>> >> Hi,
> >>> >>
> >>> >> Most of those are just warnings, the only error I see there comes
> from
> >>> >> the shell, probably an error in your script.
> >>> >>
> >>> >> Cheers,
> >>> >> --
> >>> >> Szilárd
> >>> >>
> >>> >>
> >>> >>
> >>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
> >>> >>  wrote:
> >>> >>
> >>> >> Hi users,
> >>> >>
> >>> >> Am running mdrun on gpu . I receive an error such as=
> >>> >>
> >>> >> WARNING: This run will generate roughly 38570 Mb of data
> >>> >>
> >>> >>
> >>> >> WARNING: Open

Re: [gmx-users] mdrun-gpu error

[Szilárd Páll]

That's a generic GPU kernel launch failure which can mean anything,
from faulty hardware to bad driver to messed up installation.

Does the memory test run? Try to compile/install again and see if it works.

--
Szilárd



On Thu, Jan 19, 2012 at 4:18 PM, aiswarya pawar
 wrote:
> when i tired running it again, i got an error as
>
> Cuda error in file
> '/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//bbsort.cu'
> in line 176 : unspecified launch failure.
>
> /bin/cat: file_loc: No such file or directory
>
>
> On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar 
> wrote:
>>
>> Has the tesla card got to do anything with the error. Am using Nvidia
>> Tesla S1070 1U server.
>>
>>
>> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll 
>> wrote:
>>>
>>> And sorting out where the /bin/cat error comes from because that is
>>> surely not a Gromacs message!
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>>
>>>
>>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
>>> wrote:
>>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>>> >
>>> > Mark,
>>> >
>>> > THe normal mdrun also hangs thus not generating any output.
>>> >
>>> >
>>> > OK. It's your problem to solve... keep simplifying stuff until you can
>>> > isolate a small number of possible causes. Top of the list is file
>>> > system
>>> > availability.
>>> >
>>> > Mark
>>> >
>>> >
>>> >
>>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
>>> > wrote:
>>> >>
>>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> Its going into the running mode but gets hang there for long hours
>>> >> which
>>> >> generating any data in the output file. And am not able to figure out
>>> >> the
>>> >> error file_doc. Please anyone knows what's going wrong.
>>> >>
>>> >>
>>> >> No, but you should start trying to simplify what you're doing to see
>>> >> where
>>> >> the problem lies. Does normal mdrun work?
>>> >>
>>> >> Mark
>>> >>
>>> >>
>>> >> Thanks
>>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
>>> >> for
>>> >> it!
>>> >>
>>> >> -Original Message-
>>> >> From: Szilárd Páll 
>>> >> Sender: gmx-users-boun...@gromacs.org
>>> >> Date: Wed, 18 Jan 2012 14:47:59
>>> >> To: Discussion list for GROMACS users
>>> >> Reply-To: Discussion list for GROMACS users 
>>> >> Subject: Re: [gmx-users] mdrun-gpu error
>>> >>
>>> >> Hi,
>>> >>
>>> >> Most of those are just warnings, the only error I see there comes from
>>> >> the shell, probably an error in your script.
>>> >>
>>> >> Cheers,
>>> >> --
>>> >> Szilárd
>>> >>
>>> >>
>>> >>
>>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>>> >>  wrote:
>>> >>
>>> >> Hi users,
>>> >>
>>> >> Am running mdrun on gpu . I receive an error such as=
>>> >>
>>> >> WARNING: This run will generate roughly 38570 Mb of data
>>> >>
>>> >>
>>> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>>> >> integrator.
>>> >>
>>> >>
>>> >> WARNING: OpenMM supports only Andersen thermostat with the
>>> >> md/md-vv/md-vv-avek integrators.
>>> >>
>>> >>
>>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
>>> >> coupling.
>>> >>
>>> >>
>>> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
>>> >> and
>>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>>> >> option.
>>> >>
>>> >> /bin/cat: file_loc: No such file or directory
>>> >>
>>> >>
>>> >> and the job is running but th

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

when i tired running it again, i got an error as

Cuda error in file
'/home/staff/sec/secdpal/software/openmm_tesla/platforms/cuda/./src/kernels//
bbsort.cu' in line 176 : unspecified launch failure.
/bin/cat: file_loc: No such file or directory

On Thu, Jan 19, 2012 at 8:45 PM, aiswarya pawar wrote:

> Has the tesla card got to do anything with the error. Am using Nvidia
> Tesla S1070 1U server.
>
>
> On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll wrote:
>
>> And sorting out where the /bin/cat error comes from because that is
>> surely not a Gromacs message!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
>> wrote:
>> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>> >
>> > Mark,
>> >
>> > THe normal mdrun also hangs thus not generating any output.
>> >
>> >
>> > OK. It's your problem to solve... keep simplifying stuff until you can
>> > isolate a small number of possible causes. Top of the list is file
>> system
>> > availability.
>> >
>> > Mark
>> >
>> >
>> >
>> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
>> > wrote:
>> >>
>> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>> >>
>> >> Hi,
>> >>
>> >> Its going into the running mode but gets hang there for long hours
>> which
>> >> generating any data in the output file. And am not able to figure out
>> the
>> >> error file_doc. Please anyone knows what's going wrong.
>> >>
>> >>
>> >> No, but you should start trying to simplify what you're doing to see
>> where
>> >> the problem lies. Does normal mdrun work?
>> >>
>> >> Mark
>> >>
>> >>
>> >> Thanks
>> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
>> for
>> >> it!
>> >>
>> >> -Original Message-
>> >> From: Szilárd Páll 
>> >> Sender: gmx-users-boun...@gromacs.org
>> >> Date: Wed, 18 Jan 2012 14:47:59
>> >> To: Discussion list for GROMACS users
>> >> Reply-To: Discussion list for GROMACS users 
>> >> Subject: Re: [gmx-users] mdrun-gpu error
>> >>
>> >> Hi,
>> >>
>> >> Most of those are just warnings, the only error I see there comes from
>> >> the shell, probably an error in your script.
>> >>
>> >> Cheers,
>> >> --
>> >> Szilárd
>> >>
>> >>
>> >>
>> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>> >>  wrote:
>> >>
>> >> Hi users,
>> >>
>> >> Am running mdrun on gpu . I receive an error such as=
>> >>
>> >> WARNING: This run will generate roughly 38570 Mb of data
>> >>
>> >>
>> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> >> integrator.
>> >>
>> >>
>> >> WARNING: OpenMM supports only Andersen thermostat with the
>> >> md/md-vv/md-vv-avek integrators.
>> >>
>> >>
>> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
>> coupling.
>> >>
>> >>
>> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
>> and
>> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> >> option.
>> >>
>> >> /bin/cat: file_loc: No such file or directory
>> >>
>> >>
>> >> and the job is running but the nothing written into .xtc, .trr, .edr
>> files
>> >> .
>> >> What could have gone wrong?
>> >>
>> >> --
>> >> Aiswarya  B Pawar
>> >>
>> >> Bioinformatics Dept,
>> >> Indian Institute of Science
>> >> Bangalore
>> >>
>> >>
>> >>
>> >> --
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-requ...@gromacs.org.
>> >

Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Has the tesla card got to do anything with the error. Am using Nvidia Tesla
S1070 1U server.


On Thu, Jan 19, 2012 at 8:37 PM, Szilárd Páll wrote:

> And sorting out where the /bin/cat error comes from because that is
> surely not a Gromacs message!
>
> Cheers,
> --
> Szilárd
>
>
>
> On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham 
> wrote:
> > On 19/01/2012 8:45 PM, aiswarya pawar wrote:
> >
> > Mark,
> >
> > THe normal mdrun also hangs thus not generating any output.
> >
> >
> > OK. It's your problem to solve... keep simplifying stuff until you can
> > isolate a small number of possible causes. Top of the list is file system
> > availability.
> >
> > Mark
> >
> >
> >
> > On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
> > wrote:
> >>
> >> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
> >>
> >> Hi,
> >>
> >> Its going into the running mode but gets hang there for long hours which
> >> generating any data in the output file. And am not able to figure out
> the
> >> error file_doc. Please anyone knows what's going wrong.
> >>
> >>
> >> No, but you should start trying to simplify what you're doing to see
> where
> >> the problem lies. Does normal mdrun work?
> >>
> >> Mark
> >>
> >>
> >> Thanks
> >> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go
> for
> >> it!
> >>
> >> -Original Message-
> >> From: Szilárd Páll 
> >> Sender: gmx-users-boun...@gromacs.org
> >> Date: Wed, 18 Jan 2012 14:47:59
> >> To: Discussion list for GROMACS users
> >> Reply-To: Discussion list for GROMACS users 
> >> Subject: Re: [gmx-users] mdrun-gpu error
> >>
> >> Hi,
> >>
> >> Most of those are just warnings, the only error I see there comes from
> >> the shell, probably an error in your script.
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >>
> >> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
> >>  wrote:
> >>
> >> Hi users,
> >>
> >> Am running mdrun on gpu . I receive an error such as=
> >>
> >> WARNING: This run will generate roughly 38570 Mb of data
> >>
> >>
> >> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> >> integrator.
> >>
> >>
> >> WARNING: OpenMM supports only Andersen thermostat with the
> >> md/md-vv/md-vv-avek integrators.
> >>
> >>
> >> WARNING: OpenMM supports only Monte Carlo barostat for pressure
> coupling.
> >>
> >>
> >> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE
> and
> >> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> >> option.
> >>
> >> /bin/cat: file_loc: No such file or directory
> >>
> >>
> >> and the job is running but the nothing written into .xtc, .trr, .edr
> files
> >> .
> >> What could have gone wrong?
> >>
> >> --
> >> Aiswarya  B Pawar
> >>
> >> Bioinformatics Dept,
> >> Indian Institute of Science
> >> Bangalore
> >>
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >>
> >>
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the ar

Re: [gmx-users] mdrun-gpu error

[Szilárd Páll]

And sorting out where the /bin/cat error comes from because that is
surely not a Gromacs message!

Cheers,
--
Szilárd



On Thu, Jan 19, 2012 at 1:12 PM, Mark Abraham  wrote:
> On 19/01/2012 8:45 PM, aiswarya pawar wrote:
>
> Mark,
>
> THe normal mdrun also hangs thus not generating any output.
>
>
> OK. It's your problem to solve... keep simplifying stuff until you can
> isolate a small number of possible causes. Top of the list is file system
> availability.
>
> Mark
>
>
>
> On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham 
> wrote:
>>
>> On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>>
>> Hi,
>>
>> Its going into the running mode but gets hang there for long hours which
>> generating any data in the output file. And am not able to figure out the
>> error file_doc. Please anyone knows what's going wrong.
>>
>>
>> No, but you should start trying to simplify what you're doing to see where
>> the problem lies. Does normal mdrun work?
>>
>> Mark
>>
>>
>> Thanks
>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
>> it!
>>
>> -Original Message-
>> From: Szilárd Páll 
>> Sender: gmx-users-boun...@gromacs.org
>> Date: Wed, 18 Jan 2012 14:47:59
>> To: Discussion list for GROMACS users
>> Reply-To: Discussion list for GROMACS users 
>> Subject: Re: [gmx-users] mdrun-gpu error
>>
>> Hi,
>>
>> Most of those are just warnings, the only error I see there comes from
>> the shell, probably an error in your script.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
>>  wrote:
>>
>> Hi users,
>>
>> Am running mdrun on gpu . I receive an error such as=
>>
>> WARNING: This run will generate roughly 38570 Mb of data
>>
>>
>> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
>> integrator.
>>
>>
>> WARNING: OpenMM supports only Andersen thermostat with the
>> md/md-vv/md-vv-avek integrators.
>>
>>
>> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>>
>>
>> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
>> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
>> option.
>>
>> /bin/cat: file_loc: No such file or directory
>>
>>
>> and the job is running but the nothing written into .xtc, .trr, .edr files
>> .
>> What could have gone wrong?
>>
>> --
>> Aiswarya  B Pawar
>>
>> Bioinformatics Dept,
>> Indian Institute of Science
>> Bangalore
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] mdrun-gpu error

[Mark Abraham]

On 19/01/2012 8:45 PM, aiswarya pawar wrote:

Mark,

THe normal mdrun also hangs thus not generating any output.


OK. It's your problem to solve... keep simplifying stuff until you can 
isolate a small number of possible causes. Top of the list is file 
system availability.


Mark



On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote:


On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com> wrote:

Hi,

Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.


No, but you should start trying to simplify what you're doing to
see where the problem lies. Does normal mdrun work?

Mark



Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for 
it!

-Original Message-
From: Szilárd Páll  <mailto:szilard.p...@cbr.su.se>
Sender:gmx-users-boun...@gromacs.org  <mailto:gmx-users-boun...@gromacs.org>
Date: Wed, 18 Jan 2012 14:47:59
To: Discussion list for GROMACS users  
<mailto:gmx-users@gromacs.org>
Reply-To: Discussion list for GROMACS users  
<mailto:gmx-users@gromacs.org>
Subject: Re: [gmx-users] mdrun-gpu error

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
  <mailto:aiswarya.pa...@gmail.com>  wrote:

Hi users,

Am running mdrun on gpu . I receive an error such as=

WARNING: This run will generate roughly 38570 Mb of data


WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.


WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.

/bin/cat: file_loc: No such file or directory


and the job is running but the nothing written into .xtc, .trr, .edr files .
What could have gone wrong?

--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore



--
gmx-users mailing listgmx-us...@gromacs.org  <mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search  before posting!
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Please search the archive 
athttp://www.gromacs.org/Support/Mailing_Lists/Search  before posting!
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<mailto:gmx-users-requ...@gromacs.org>.
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--
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<mailto:gmx-users@gromacs.org>
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Please search the archive at
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--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore






-- 
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Re: [gmx-users] mdrun-gpu error

[aiswarya pawar]

Mark,

THe normal mdrun also hangs thus not generating any output.

On Thu, Jan 19, 2012 at 3:09 AM, Mark Abraham wrote:

>  On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:
>
> Hi,
>
> Its going into the running mode but gets hang there for long hours which 
> generating any data in the output file. And am not able to figure out the 
> error file_doc. Please anyone knows what's going wrong.
>
>
> No, but you should start trying to simplify what you're doing to see where
> the problem lies. Does normal mdrun work?
>
> Mark
>
>
>  Thanks
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>
> -Original Message-
> From: Szilárd Páll  
> Sender: gmx-users-boun...@gromacs.org
> Date: Wed, 18 Jan 2012 14:47:59
> To: Discussion list for GROMACS users 
> 
> Reply-To: Discussion list for GROMACS users  
> 
> Subject: Re: [gmx-users] mdrun-gpu error
>
> Hi,
>
> Most of those are just warnings, the only error I see there comes from
> the shell, probably an error in your script.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar 
>  wrote:
>
>  Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will generate roughly 38570 Mb of data
>
>
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
>
>
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
>
>
> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>
>
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
>
> /bin/cat: file_loc: No such file or directory
>
>
> and the job is running but the nothing written into .xtc, .trr, .edr files .
> What could have gone wrong?
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
> --
> gmx-users mailing list
> gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive 
> athttp://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>  --
> gmx-users mailing list
> gmx-users@gromacs.orghttp://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] mdrun-gpu error

[Mark Abraham]

On 19/01/2012 2:59 AM, aiswarya.pa...@gmail.com wrote:

Hi,

Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.


No, but you should start trying to simplify what you're doing to see 
where the problem lies. Does normal mdrun work?


Mark



Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Szilárd Páll
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 18 Jan 2012 14:47:59
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdrun-gpu error

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
  wrote:

Hi users,

Am running mdrun on gpu . I receive an error such as=

WARNING: This run will generate roughly 38570 Mb of data


WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.


WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.

/bin/cat: file_loc: No such file or directory


and the job is running but the nothing written into .xtc, .trr, .edr files .
What could have gone wrong?

--
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore



--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] mdrun-gpu error

[aiswarya . pawar]

Hi, 

Its going into the running mode but gets hang there for long hours which 
generating any data in the output file. And am not able to figure out the error 
file_doc. Please anyone knows what's going wrong.

Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Szilárd Páll 
Sender: gmx-users-boun...@gromacs.org
Date: Wed, 18 Jan 2012 14:47:59 
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] mdrun-gpu error

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
 wrote:
> Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will generate roughly 38570 Mb of data
>
>
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
>
>
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
>
>
> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>
>
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
>
> /bin/cat: file_loc: No such file or directory
>
>
> and the job is running but the nothing written into .xtc, .trr, .edr files .
> What could have gone wrong?
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
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Re: [gmx-users] mdrun-gpu error

[Szilárd Páll]

Hi,

Most of those are just warnings, the only error I see there comes from
the shell, probably an error in your script.

Cheers,
--
Szilárd



On Wed, Jan 18, 2012 at 12:27 PM, aiswarya pawar
 wrote:
> Hi users,
>
> Am running mdrun on gpu . I receive an error such as=
>
> WARNING: This run will generate roughly 38570 Mb of data
>
>
> WARNING: OpenMM does not support leap-frog, will use velocity-verlet
> integrator.
>
>
> WARNING: OpenMM supports only Andersen thermostat with the
> md/md-vv/md-vv-avek integrators.
>
>
> WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.
>
>
> WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
> CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
> option.
>
> /bin/cat: file_loc: No such file or directory
>
>
> and the job is running but the nothing written into .xtc, .trr, .edr files .
> What could have gone wrong?
>
> --
> Aiswarya  B Pawar
>
> Bioinformatics Dept,
> Indian Institute of Science
> Bangalore
>
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] mdrun-gpu error

[aiswarya pawar]

Hi users,

Am running mdrun on gpu . I receive an error such as=

WARNING: This run will generate roughly 38570 Mb of data


WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.


WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.

/bin/cat: file_loc: No such file or directory


and the job is running but the nothing written into .xtc, .trr, .edr files
. What could have gone wrong?

-- 
Aiswarya  B Pawar

Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Re: [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

[H.Ghorbanfekr]

I used the newest version of gromacs 4.5.4 (and not install beta gpu version
) so everything goes well.
thanks for your reply

On Sun, Aug 14, 2011 at 5:52 PM, Justin A. Lemkul  wrote:

>
>
> H.Ghorbanfekr wrote:
>
>> Hi ,
>>
>> I'm using mdrun-gpu  for testing gpubench demos.
>> But I've got this error message:
>>
>> Fatal error:
>> reading tpx file (topol.tpr) version 73 with version 71 program
>>
>> I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta
>> 1, 2 versions.  But it still doesn't work. any idea on this?
>>
>>
> Gromacs programs are backwards-compatible, but if the .tpr file version has
> changed between revisions, they are not forward-compatible.  A version 73
> .tpr file is from Gromacs version 4.5.4, so the error comes when you try to
> use an older Gromacs version to run it.  Stick with one version of Gromacs
> (preferrably the newest) and use it for everything.  Having multiple
> versions lying around unnecessarily can be problematic when you might wind
> up using executables from different installations.
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> Support/Mailing_Lists/Searchbefore
>  posting!
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> Can't post? Read 
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Re: [gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

[Justin A. Lemkul]

H.Ghorbanfekr wrote:

Hi ,

I'm using mdrun-gpu  for testing gpubench demos.
But I've got this error message:

Fatal error:
reading tpx file (topol.tpr) version 73 with version 71 program

I installed different version of gromacs 4.5 to 4.5.4 and 
gpu-gromacs-beta 1, 2 versions.  
But it still doesn't work. any idea on this?




Gromacs programs are backwards-compatible, but if the .tpr file version has 
changed between revisions, they are not forward-compatible.  A version 73 .tpr 
file is from Gromacs version 4.5.4, so the error comes when you try to use an 
older Gromacs version to run it.  Stick with one version of Gromacs (preferrably 
the newest) and use it for everything.  Having multiple versions lying around 
unnecessarily can be problematic when you might wind up using executables from 
different installations.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] mdrun-gpu, fatal error: reading tpx file (topol.tpr) version 73 with version 71 program

[H.Ghorbanfekr]

Hi ,

I'm using mdrun-gpu  for testing gpubench demos.
But I've got this error message:

Fatal error:
reading tpx file (topol.tpr) version 73 with version 71 program

I installed different version of gromacs 4.5 to 4.5.4 and gpu-gromacs-beta
1, 2 versions.
But it still doesn't work. any idea on this?

thanks
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Re: [gmx-users] mdrun-gpu

[Szilárd Páll]

Dear Natalia,

The current mdrun-gpu (which btw uses OpenMM) is capable to run a
single simulation, on a single node, using a single GPU only.

Cheers,
--
Szilárd



On Fri, Mar 4, 2011 at 6:28 PM, Nathalia Garces  wrote:
> Hello,
> I want to know if it is possible to use "mdrun-gpu" with the command
> "-multi", meaning to use GPUs using paralell simulation.
> When I used it (mdrun-gpu -multi 2 -replex 2 ), it appears me an error shown
> bellow
>  Fatal error:
> This binary is compiled without MPI support, can not do multiple
> simulations.
>
> this bewilder me because I'm not sure I can use gpu and mpi at the same
> time.
>
>
> Thank you for four answer
>
> Nathalia
>
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[gmx-users] mdrun-gpu

[Nathalia Garces]

Hello,
I want to know if it is possible to use "mdrun-gpu" with the command
"-multi", meaning to use GPUs using paralell simulation.
When I used it (mdrun-gpu -multi 2 -replex 2 ), it appears me an error shown
bellow
* Fatal error:
This binary is compiled without MPI support, can not do multiple
simulations.*

this bewilder me because I'm not sure I can use gpu and mpi at the same
time.


Thank you for four answer

Nathalia
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Re: [gmx-users] ./mdrun-gpu fatal error

[Szilárd Páll]

You can try the systems we provided on the GROMACS-GPU page:
http://www.gromacs.org/gpu#GPU_Benchmarks

--
Szilárd




On Sat, Nov 6, 2010 at 12:59 AM, lin hen  wrote:
> Yeah, I think my problem is the input, but I don't have the .mpd file,  I am
> using the existing input which has no problem with Gromacs 4.0.5
> using ./mdrun-openmm.
>
> So is there any other way I could modify?
> Thanks,
>
> YY
>
>> Date: Fri, 5 Nov 2010 19:54:10 -0400
>> From: jalem...@vt.edu
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>>
>>
>>
>> lin hen wrote:
>> > Thanks a lot for your reply, I didn't have this .mdp file, and I
>> > attached the log file, how to modify?
>> >
>>
>> You don't have an .mdp file? Then how did you create your input .tpr file?
>> This is the only way to fix your problem - specify proper input parameters
>> in
>> the .mdp file.
>>
>> > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the
>> > requirements listed for gcc is 4.4, is it a problem?
>> >
>>
>> I think there have been some issues associated with gcc-4.1.x, but I am
>> not sure
>> that they were specifically related to the compiler or some
>> incompatibility with
>> the code that was addressed. In any case, your compiler is not your
>> problem.
>> You have an error in your input file, and the fatal error is very clear
>> about this.
>>
>> -Justin
>>
>> > Thanks,
>> >
>> > yy
>> >
>> > > Date: Fri, 5 Nov 2010 19:29:09 -0400
>> > > From: jalem...@vt.edu
>> > > To: gmx-users@gromacs.org
>> > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
>> > >
>> > >
>> > >
>> > > lin hen wrote:
>> > > > Hi,
>> > > >
>> > > > I am new for gromacs, I am trying to run the mdrun-gpu executable:
>> > > >
>> > > > the step to build the mdrun-gpu:
>> > > >
>> > > > 1. disable the shared libraries:
>> > > > //disable shared libraries (can be problematic with MPI, Windows)
>> > > > BUILD_SHARED_LIBS:BOOL=OFF
>> > > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$
>> > LD_LIBRARY_PATH
>> > > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
>> > > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
>> > > > 5. ./configure
>> > > > 6. cmake -DGMX_OPENMM=ON
>> > > > 7. make mdrun
>> > > > 8. make install
>> > > >
>> > > > when I got the mdrun-gpu in /src/kernel.
>> > > >
>> > > > I put all the shared libs in one folder, point the LD_LIBRARY_PATH
>> > > > to
>> > > > this folder, also openmm libs
>> > > >
>> > > > The attached is the .tpr file I use in the same folder with
>> > > > mdrun-gpu.
>> > > >
>> > > > when i run ./mdrun-gpu
>> > > > it shows:
>> > > >
>> > > > :-) G R O M A C S (-:
>> > > > GROningen MAchine for Chemical Simulation
>> > > > :-) VERSION 4.5.1 (-:
>> > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>> > > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
>> > > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
>> > > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
>> > > > Michael Shirts, Alfons Sijbers, Peter Tieleman,
>> > > > Berk Hess, David van der Spoel, and Erik Lindahl.
>> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> > > > Copyright (c) 2001-2010, The GROMACS development team at
>> > > > Uppsala University & The Royal Institute of Technology, Sweden.
>> > > > check out http://www.gromacs.org <http://www.gromacs.org/>
>> > > > for more information.
>> > > > This program is free software; you can redistribute it and/or
>> > > > modify it under the terms of the GNU General Public License
>> > > > as published by the Free Software Foundation; either version 2
>> > > > of the License, or (at your option) any later version.
>> > > > :-) ./mdrun-gpu (-:
>> > > > Option Filename Type Description
>> > > > -

Re: [gmx-users] ./mdrun-gpu fatal error

[Justin A. Lemkul]

lin hen wrote:
Yeah, I think my problem is the input, but I don't have the .mpd file,  
I am using the existing input which has no problem with Gromacs 4.0.5 
using ./mdrun-openmm.
 
So is there any other way I could modify?


No.  You need to generate a sensible input file.

-Justin


Thanks,
 
YY
 
 > Date: Fri, 5 Nov 2010 19:54:10 -0400

 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
 >
 >
 >
 > lin hen wrote:
 > > Thanks a lot for your reply, I didn't have this .mdp file, and I
 > > attached the log file, how to modify?
 > >
 >
 > You don't have an .mdp file? Then how did you create your input .tpr 
file?
 > This is the only way to fix your problem - specify proper input 
parameters in

 > the .mdp file.
 >
 > > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the
 > > requirements listed for gcc is 4.4, is it a problem?
 > >
 >
 > I think there have been some issues associated with gcc-4.1.x, but I 
am not sure
 > that they were specifically related to the compiler or some 
incompatibility with
 > the code that was addressed. In any case, your compiler is not your 
problem.
 > You have an error in your input file, and the fatal error is very 
clear about this.

 >
 > -Justin
 >
 > > Thanks,
 > >
 > > yy
 > >
 > > > Date: Fri, 5 Nov 2010 19:29:09 -0400
 > > > From: jalem...@vt.edu
 > > > To: gmx-users@gromacs.org
 > > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
 > > >
 > > >
 > > >
 > > > lin hen wrote:
 > > > > Hi,
 > > > >
 > > > > I am new for gromacs, I am trying to run the mdrun-gpu executable:
 > > > >
 > > > > the step to build the mdrun-gpu:
 > > > >
 > > > > 1. disable the shared libraries:
 > > > > //disable shared libraries (can be problematic with MPI, Windows)
 > > > > BUILD_SHARED_LIBS:BOOL=OFF
 > > > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$
 > > LD_LIBRARY_PATH
 > > > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
 > > > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
 > > > > 5. ./configure
 > > > > 6. cmake -DGMX_OPENMM=ON
 > > > > 7. make mdrun
 > > > > 8. make install
 > > > >
 > > > > when I got the mdrun-gpu in /src/kernel.
 > > > >
 > > > > I put all the shared libs in one folder, point the 
LD_LIBRARY_PATH to

 > > > > this folder, also openmm libs
 > > > >
 > > > > The attached is the .tpr file I use in the same folder with 
mdrun-gpu.

 > > > >
 > > > > when i run ./mdrun-gpu
 > > > > it shows:
 > > > >
 > > > > :-) G R O M A C S (-:
 > > > > GROningen MAchine for Chemical Simulation
 > > > > :-) VERSION 4.5.1 (-:
 > > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
 > > > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 > > > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
 > > > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
 > > > > Michael Shirts, Alfons Sijbers, Peter Tieleman,
 > > > > Berk Hess, David van der Spoel, and Erik Lindahl.
 > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 > > > > Copyright (c) 2001-2010, The GROMACS development team at
 > > > > Uppsala University & The Royal Institute of Technology, Sweden.
 > > > > check out http://www.gromacs.org <http://www.gromacs.org/>
 > > > > for more information.
 > > > > This program is free software; you can redistribute it and/or
 > > > > modify it under the terms of the GNU General Public License
 > > > > as published by the Free Software Foundation; either version 2
 > > > > of the License, or (at your option) any later version.
 > > > > :-) ./mdrun-gpu (-:
 > > > > Option Filename Type Description
 > > > > 
 > > > > -s topol.tpr Input Run input file: tpr tpb tpa
 > > > > -o traj.trr Output Full precision trajectory: trr trj cpt
 > > > > -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
 > > > > format)
 > > > > -cpi state.cpt Input, Opt. Checkpoint file
 > > > > -cpo state.cpt Output, Opt. Checkpoint file
 > > > > -c confout.gro Output S

RE: [gmx-users] ./mdrun-gpu fatal error

[lin hen]

Yeah, I think my problem is the input, but I don't have the .mpd file,  I am 
using the existing input which has no problem with Gromacs 4.0.5 using 
./mdrun-openmm.
 
So is there any other way I could modify?
Thanks,
 
YY
 
> Date: Fri, 5 Nov 2010 19:54:10 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] ./mdrun-gpu fatal error
> 
> 
> 
> lin hen wrote:
> > Thanks a lot for your reply, I didn't have this .mdp file, and I 
> > attached the log file, how to modify?
> > 
> 
> You don't have an .mdp file? Then how did you create your input .tpr file? 
> This is the only way to fix your problem - specify proper input parameters in 
> the .mdp file.
> 
> > Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the 
> > requirements listed for gcc is 4.4, is it a problem?
> > 
> 
> I think there have been some issues associated with gcc-4.1.x, but I am not 
> sure 
> that they were specifically related to the compiler or some incompatibility 
> with 
> the code that was addressed. In any case, your compiler is not your problem. 
> You have an error in your input file, and the fatal error is very clear about 
> this.
> 
> -Justin
> 
> > Thanks,
> > 
> > yy
> > 
> > > Date: Fri, 5 Nov 2010 19:29:09 -0400
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
> > >
> > >
> > >
> > > lin hen wrote:
> > > > Hi,
> > > >
> > > > I am new for gromacs, I am trying to run the mdrun-gpu executable:
> > > >
> > > > the step to build the mdrun-gpu:
> > > >
> > > > 1. disable the shared libraries:
> > > > //disable shared libraries (can be problematic with MPI, Windows)
> > > > BUILD_SHARED_LIBS:BOOL=OFF
> > > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ 
> > LD_LIBRARY_PATH
> > > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
> > > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
> > > > 5. ./configure
> > > > 6. cmake -DGMX_OPENMM=ON
> > > > 7. make mdrun
> > > > 8. make install
> > > >
> > > > when I got the mdrun-gpu in /src/kernel.
> > > >
> > > > I put all the shared libs in one folder, point the LD_LIBRARY_PATH to
> > > > this folder, also openmm libs
> > > >
> > > > The attached is the .tpr file I use in the same folder with mdrun-gpu.
> > > >
> > > > when i run ./mdrun-gpu
> > > > it shows:
> > > >
> > > > :-) G R O M A C S (-:
> > > > GROningen MAchine for Chemical Simulation
> > > > :-) VERSION 4.5.1 (-:
> > > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
> > > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> > > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
> > > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
> > > > Michael Shirts, Alfons Sijbers, Peter Tieleman,
> > > > Berk Hess, David van der Spoel, and Erik Lindahl.
> > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > > > Copyright (c) 2001-2010, The GROMACS development team at
> > > > Uppsala University & The Royal Institute of Technology, Sweden.
> > > > check out http://www.gromacs.org <http://www.gromacs.org/>
> > > > for more information.
> > > > This program is free software; you can redistribute it and/or
> > > > modify it under the terms of the GNU General Public License
> > > > as published by the Free Software Foundation; either version 2
> > > > of the License, or (at your option) any later version.
> > > > :-) ./mdrun-gpu (-:
> > > > Option Filename Type Description
> > > > 
> > > > -s topol.tpr Input Run input file: tpr tpb tpa
> > > > -o traj.trr Output Full precision trajectory: trr trj cpt
> > > > -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
> > > > format)
> > > > -cpi state.cpt Input, Opt. Checkpoint file
> > > > -cpo state.cpt Output, Opt. Checkpoint file
> > > > -c confout.gro Output Structure file: gro g96 pdb etc.
> > > > -e ener.edr Output Energy file
> > > > -g md.log Output Log file
> > > > -dhdl dhdl.

Re: [gmx-users] ./mdrun-gpu fatal error

[Justin A. Lemkul]

lin hen wrote:
Thanks a lot for your reply, I didn't have this .mdp file, and I 
attached the log file, how to modify?
 


You don't have an .mdp file?  Then how did you create your input .tpr file? 
This is the only way to fix your problem - specify proper input parameters in 
the .mdp file.


Just wonder the gcc compiler, I am using gcc 4.1.2, but I saw the 
requirements listed for gcc is 4.4, is it a problem?
 


I think there have been some issues associated with gcc-4.1.x, but I am not sure 
that they were specifically related to the compiler or some incompatibility with 
the code that was addressed.  In any case, your compiler is not your problem. 
You have an error in your input file, and the fatal error is very clear about this.


-Justin


Thanks,
 
yy
 
 > Date: Fri, 5 Nov 2010 19:29:09 -0400

 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] ./mdrun-gpu fatal error
 >
 >
 >
 > lin hen wrote:
 > > Hi,
 > >
 > > I am new for gromacs, I am trying to run the mdrun-gpu executable:
 > >
 > > the step to build the mdrun-gpu:
 > >
 > > 1. disable the shared libraries:
 > > //disable shared libraries (can be problematic with MPI, Windows)
 > > BUILD_SHARED_LIBS:BOOL=OFF
 > > 2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ 
LD_LIBRARY_PATH

 > > 3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
 > > 4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
 > > 5. ./configure
 > > 6. cmake -DGMX_OPENMM=ON
 > > 7. make mdrun
 > > 8. make install
 > >
 > > when I got the mdrun-gpu in /src/kernel.
 > >
 > > I put all the shared libs in one folder, point the LD_LIBRARY_PATH to
 > > this folder, also openmm libs
 > >
 > > The attached is the .tpr file I use in the same folder with mdrun-gpu.
 > >
 > > when i run ./mdrun-gpu
 > > it shows:
 > >
 > > :-) G R O M A C S (-:
 > > GROningen MAchine for Chemical Simulation
 > > :-) VERSION 4.5.1 (-:
 > > Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
 > > Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 > > Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
 > > Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
 > > Michael Shirts, Alfons Sijbers, Peter Tieleman,
 > > Berk Hess, David van der Spoel, and Erik Lindahl.
 > > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 > > Copyright (c) 2001-2010, The GROMACS development team at
 > > Uppsala University & The Royal Institute of Technology, Sweden.
 > > check out http://www.gromacs.org <http://www.gromacs.org/>
 > > for more information.
 > > This program is free software; you can redistribute it and/or
 > > modify it under the terms of the GNU General Public License
 > > as published by the Free Software Foundation; either version 2
 > > of the License, or (at your option) any later version.
 > > :-) ./mdrun-gpu (-:
 > > Option Filename Type Description
 > > 
 > > -s topol.tpr Input Run input file: tpr tpb tpa
 > > -o traj.trr Output Full precision trajectory: trr trj cpt
 > > -x traj.xtc Output, Opt. Compressed trajectory (portable xdr
 > > format)
 > > -cpi state.cpt Input, Opt. Checkpoint file
 > > -cpo state.cpt Output, Opt. Checkpoint file
 > > -c confout.gro Output Structure file: gro g96 pdb etc.
 > > -e ener.edr Output Energy file
 > > -g md.log Output Log file
 > > -dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
 > > -field field.xvg Output, Opt. xvgr/xmgr file
 > > -table table.xvg Input, Opt. xvgr/xmgr file
 > > -tablep tablep.xvg Input, Opt. xvgr/xmgr file
 > > -tableb table.xvg Input, Opt. xvgr/xmgr file
 > > -rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
 > > -tpi tpi.xvg Output, Opt. xvgr/xmgr file
 > > -tpid tpidist.xvg Output, Opt. xvgr/xmgr file
 > > -ei sam.edi Input, Opt. ED sampling input
 > > -eo sam.edo Output, Opt. ED sampling output
 > > -j wham.gct Input, Opt. General coupling stuff
 > > -jo bam.gct Output, Opt. General coupling stuff
 > > -ffout gct.xvg Output, Opt. xvgr/xmgr file
 > > -devout deviatie.xvg Output, Opt. xvgr/xmgr file
 > > -runav runaver.xvg Output, Opt. xvgr/xmgr file
 > > -px pullx.xvg Output, Opt. xvgr/xmgr file
 > > -pf pullf.xvg Output, Opt. xvgr/xmgr file
 > > -mtx nm.mtx Output, Opt. Hessian matrix
 > > -dn dipole.ndx Output, Opt. Index file
 > > Option Type Value Description
 > > --
 > > -[no]h bool no

Re: [gmx-users] ./mdrun-gpu fatal error

[Justin A. Lemkul]

lin hen wrote:

Hi,
 
I am new for gromacs, I am trying to run the mdrun-gpu executable:
 
the step to build the mdrun-gpu:
 
1. disable the shared libraries:

   //disable shared libraries (can be problematic with MPI, Windows)
BUILD_SHARED_LIBS:BOOL=OFF
2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ LD_LIBRARY_PATH
3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
5. ./configure
6. cmake -DGMX_OPENMM=ON
7. make mdrun
8. make install
 
when I got the mdrun-gpu in /src/kernel.
 
I put all the shared libs in one folder, point the LD_LIBRARY_PATH to 
this folder, also openmm libs
 
The attached is the .tpr file I use in the same folder with mdrun-gpu.
 
when i run ./mdrun-gpu

it shows:

 :-)  G  R  O  M  A  C  S  (-:
   GROningen MAchine for Chemical Simulation
:-)  VERSION 4.5.1  (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
  Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
   Berk Hess, David van der Spoel, and Erik Lindahl.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org  
for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.
 :-)  ./mdrun-gpu  (-:
Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr 
format)

-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file
Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or 
cartesian

-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions 
with

DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no 
or yes

-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction

[gmx-users] ./mdrun-gpu fatal error

[lin hen]

Hi,
 
I am new for gromacs, I am trying to run the mdrun-gpu executable:
 
the step to build the mdrun-gpu:
 
1. disable the shared libraries:
   //disable shared libraries (can be problematic with MPI, Windows)
BUILD_SHARED_LIBS:BOOL=OFF
2. export LD_LIBRARY_PATH=/path to openmm2.0-Linux64/lib:$ LD_LIBRARY_PATH
3. export OPENMM_PLUGIN_DIR=/path to openmm2.0-Linux64/plugins
4. export OPENMM_ROOT_DIR=/path to openmm2.0-Linux64
5. ./configure
6. cmake -DGMX_OPENMM=ON
7. make mdrun
8. make install
 
when I got the mdrun-gpu in /src/kernel. 
 
I put all the shared libs in one folder, point the LD_LIBRARY_PATH to this 
folder, also openmm libs
 
The attached is the .tpr file I use in the same folder with mdrun-gpu.
 
when i run ./mdrun-gpu
it shows:

 :-)  G  R  O  M  A  C  S  (-:
   GROningen MAchine for Chemical Simulation
:-)  VERSION 4.5.1  (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Peiter Meulenhoff,
  Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schultz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
   Berk Hess, David van der Spoel, and Erik Lindahl.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.
 :-)  ./mdrun-gpu  (-:
Option Filename  Type Description

  -s  topol.tpr  InputRun input file: tpr tpb tpa
  -o   traj.trr  Output   Full precision trajectory: trr trj cpt
  -x   traj.xtc  Output, Opt. Compressed trajectory (portable xdr format)
-cpi  state.cpt  Input, Opt.  Checkpoint file
-cpo  state.cpt  Output, Opt. Checkpoint file
  -cconfout.gro  Output   Structure file: gro g96 pdb etc.
  -e   ener.edr  Output   Energy file
  -g md.log  Output   Log file
-dhdl  dhdl.xvg  Output, Opt. xvgr/xmgr file
-fieldfield.xvg  Output, Opt. xvgr/xmgr file
-tabletable.xvg  Input, Opt.  xvgr/xmgr file
-tablep  tablep.xvg  Input, Opt.  xvgr/xmgr file
-tableb   table.xvg  Input, Opt.  xvgr/xmgr file
-rerunrerun.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpitpi.xvg  Output, Opt. xvgr/xmgr file
-tpid   tpidist.xvg  Output, Opt. xvgr/xmgr file
 -eisam.edi  Input, Opt.  ED sampling input
 -eosam.edo  Output, Opt. ED sampling output
  -j   wham.gct  Input, Opt.  General coupling stuff
 -jobam.gct  Output, Opt. General coupling stuff
-ffout  gct.xvg  Output, Opt. xvgr/xmgr file
-devout   deviatie.xvg  Output, Opt. xvgr/xmgr file
-runav  runaver.xvg  Output, Opt. xvgr/xmgr file
 -px  pullx.xvg  Output, Opt. xvgr/xmgr file
 -pf  pullf.xvg  Output, Opt. xvgr/xmgr file
-mtx nm.mtx  Output, Opt. Hessian matrix
 -dn dipole.ndx  Output, Opt. Index file
Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint0   Set the nicelevel
-deffnm  string Set the default filename for all file options
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-[no]pd  bool   no  Use particle decompostion
-dd  vector 0 0 0   Domain decomposition grid, 0 is optimize
-npmeint-1  Number of separate nodes to be used for PME, -1
is guess
-ddorder enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes Check for all bonded interactions with DD
-rdd real   0   The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rconreal   0   Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum   autoDynamic load balancing (with DD): auto, no or yes
-dds real   0.8 Minimum allowed dlb scaling of the DD cell size
-gcomint-1  Global communication frequency
-[no]v   bool   no  Be loud and noisy
-[no]compact bool   yes Write a compact log file
-[no]seppot  bool   no  Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce  real   -

Re: [gmx-users] mdrun-gpu error

[Renato Freitas]

Hi Roland,

I did as you suggested and it worked fine!

Thanks,

Renato


2010/10/15 Roland Schulz :
> You should use the latest GROMACS version also for the GPU. Thus compile the
> 4.5.1 for the GPU and run this.
>
> On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas  wrote:
>>
>> Hi there,
>> I have installed the gromacs-4.5.1 and it was running without
>> problems. Also I installed the GPU version of GROMACS
>> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
>> NVIDIA driver are installed. Then I tried to run the test provided by
>> Alan with the mdrun-gpu and I got an error.
>>
>> # To test mdrun-gpu
>>
>> cat << EOF >| em.mdp
>> define                   = -DFLEXIBLE
>> integrator               = cg ; steep
>> nsteps                   = 200
>> constraints              = none
>> emtol                    = 1000.0
>> nstcgsteep               = 10 ; do a steep every 10 steps of cg
>> emstep                   = 0.01 ; used with steep
>> nstcomm                  = 1
>> coulombtype              = PME
>> ns_type                  = grid
>> rlist                    = 1.0
>> rcoulomb                 = 1.0
>> rvdw                     = 1.4
>> Tcoupl                   = no
>> Pcoupl                   = no
>> gen_vel                  = no
>> nstxout                  = 0 ; write coords every # step
>> optimize_fft             = yes
>> EOF
>>
>> cat << EOF >| md.mdp
>> integrator               = md-vv
>> nsteps                   = 1000
>> dt                       = 0.002
>> constraints              = all-bonds
>> constraint-algorithm     = shake
>> nstcomm                  = 1
>> nstcalcenergy            = 1
>> ns_type                  = grid
>> rlist                    = 1.3
>> rcoulomb                 = 1.3
>> rvdw                     = 1.3
>> vdwtype                  = cut-off
>> coulombtype              = PME
>> Tcoupl                   = Andersen
>> nsttcouple               = 1
>> tau_t                    = 0.1
>> tc-grps                  = system
>> ref_t                    = 300
>> Pcoupl                   = mttk
>> Pcoupltype               = isotropic
>> nstpcouple               = 1
>> tau_p                    = 0.5
>> compressibility          = 4.5e-5
>> ref_p                    = 1.0
>> gen_vel                  = yes
>> nstxout                  = 2 ; write coords every # step
>> lincs-iter               = 2
>> DispCorr                 = EnerPres
>> optimize_fft             = yes
>> EOF
>>
>> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
>>
>> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce
>> -ignh
>>
>> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
>>
>> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
>>
>> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
>>
>> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
>> Prot.top -norandom
>>
>> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
>>
>> mdrun -v -deffnm em
>>
>> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
>>
>> mdrun-gpu -v -deffnm md -device
>> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>>
>> ---
>> Getting Loaded...
>> Reading file md.tpr, VERSION 4.5 (single precision)
>>
>> ---
>> Program mdrun-gpu, VERSION 4.5-GPU-beta2
>> Source code file:
>> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
>> line: 1971
>>
>> Fatal error:
>> reading tpx file (md.tpr) version 73 with version 71 program
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> I also have tried to use my own system to test the mdrun-gpu and I got
>> the same error.
>> Any ideas?
>>
>> Thanks,
>>
>> Renato
>> --
>> gmx-users mailing list    gmx-us...@gromacs.org
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>
>
>
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>
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RE: [gmx-users] mdrun-gpu error

[Osmair Oliveira]

Hi Renato,
 >Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program

This error occur because you are using different version of the gromacs.
Are you sure that the version of the grompp is the same of the mdrun

I hope this help.

Prof. Dr. Osmair V. Oliveira
Federal Institute of Espirito Santo
Brazil

> Date: Fri, 15 Oct 2010 17:16:00 -0300
> From: renato...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] mdrun-gpu error
> 
> Hi there,
> I have installed the gromacs-4.5.1 and it was running without
> problems. Also I installed the GPU version of GROMACS
> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
> NVIDIA driver are installed. Then I tried to run the test provided by
> Alan with the mdrun-gpu and I got an error.
> 
> # To test mdrun-gpu
> 
> cat << EOF >| em.mdp
> define   = -DFLEXIBLE
> integrator   = cg ; steep
> nsteps   = 200
> constraints  = none
> emtol= 1000.0
> nstcgsteep   = 10 ; do a steep every 10 steps of cg
> emstep   = 0.01 ; used with steep
> nstcomm  = 1
> coulombtype  = PME
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 0 ; write coords every # step
> optimize_fft = yes
> EOF
> 
> cat << EOF >| md.mdp
> integrator   = md-vv
> nsteps   = 1000
> dt   = 0.002
> constraints  = all-bonds
> constraint-algorithm = shake
> nstcomm  = 1
> nstcalcenergy= 1
> ns_type  = grid
> rlist= 1.3
> rcoulomb = 1.3
> rvdw = 1.3
> vdwtype  = cut-off
> coulombtype  = PME
> Tcoupl   = Andersen
> nsttcouple   = 1
> tau_t= 0.1
> tc-grps  = system
> ref_t= 300
> Pcoupl   = mttk
> Pcoupltype   = isotropic
> nstpcouple   = 1
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> nstxout  = 2 ; write coords every # step
> lincs-iter   = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
> 
> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
> 
> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh
> 
> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
> 
> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
> 
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
> 
> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
> Prot.top -norandom
> 
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
> 
> mdrun -v -deffnm em
> 
> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
> 
> mdrun-gpu -v -deffnm md -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
> 
> ---
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5 (single precision)
> 
> ---
> Program mdrun-gpu, VERSION 4.5-GPU-beta2
> Source code file:
> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
> line: 1971
> 
> Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> I also have tried to use my own system to test the mdrun-gpu and I got
> the same error.
> Any ideas?
> 
> Thanks,
> 
> Renato
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] mdrun-gpu error

[Roland Schulz]

You should use the latest GROMACS version also for the GPU. Thus compile the
4.5.1 for the GPU and run this.

On Fri, Oct 15, 2010 at 4:16 PM, Renato Freitas  wrote:

> Hi there,
> I have installed the gromacs-4.5.1 and it was running without
> problems. Also I installed the GPU version of GROMACS
> (gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
> NVIDIA driver are installed. Then I tried to run the test provided by
> Alan with the mdrun-gpu and I got an error.
>
> # To test mdrun-gpu
>
> cat << EOF >| em.mdp
> define   = -DFLEXIBLE
> integrator   = cg ; steep
> nsteps   = 200
> constraints  = none
> emtol= 1000.0
> nstcgsteep   = 10 ; do a steep every 10 steps of cg
> emstep   = 0.01 ; used with steep
> nstcomm  = 1
> coulombtype  = PME
> ns_type  = grid
> rlist= 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl   = no
> Pcoupl   = no
> gen_vel  = no
> nstxout  = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
> cat << EOF >| md.mdp
> integrator   = md-vv
> nsteps   = 1000
> dt   = 0.002
> constraints  = all-bonds
> constraint-algorithm = shake
> nstcomm  = 1
> nstcalcenergy= 1
> ns_type  = grid
> rlist= 1.3
> rcoulomb = 1.3
> rvdw = 1.3
> vdwtype  = cut-off
> coulombtype  = PME
> Tcoupl   = Andersen
> nsttcouple   = 1
> tau_t= 0.1
> tc-grps  = system
> ref_t= 300
> Pcoupl   = mttk
> Pcoupltype   = isotropic
> nstpcouple   = 1
> tau_p= 0.5
> compressibility  = 4.5e-5
> ref_p= 1.0
> gen_vel  = yes
> nstxout  = 2 ; write coords every # step
> lincs-iter   = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
> wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb
>
> pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh
>
> editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0
>
> genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr
>
> echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
> Prot.top -norandom
>
> grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr
>
> mdrun -v -deffnm em
>
> grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr
>
> mdrun-gpu -v -deffnm md -device
> "OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"
>
> ---
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5 (single precision)
>
> ---
> Program mdrun-gpu, VERSION 4.5-GPU-beta2
> Source code file:
> /home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
> line: 1971
>
> Fatal error:
> reading tpx file (md.tpr) version 73 with version 71 program
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> I also have tried to use my own system to test the mdrun-gpu and I got
> the same error.
> Any ideas?
>
> Thanks,
>
> Renato
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
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865-241-1537, ORNL PO BOX 2008 MS6309
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[gmx-users] mdrun-gpu error

[Renato Freitas]

Hi there,
I have installed the gromacs-4.5.1 and it was running without
problems. Also I installed the GPU version of GROMACS
(gromacs-4.5-GPU-beta2). I have a GTX 480, and the CUDA libraries and
NVIDIA driver are installed. Then I tried to run the test provided by
Alan with the mdrun-gpu and I got an error.

# To test mdrun-gpu

cat << EOF >| em.mdp
define   = -DFLEXIBLE
integrator   = cg ; steep
nsteps   = 200
constraints  = none
emtol= 1000.0
nstcgsteep   = 10 ; do a steep every 10 steps of cg
emstep   = 0.01 ; used with steep
nstcomm  = 1
coulombtype  = PME
ns_type  = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 0 ; write coords every # step
optimize_fft = yes
EOF

cat << EOF >| md.mdp
integrator   = md-vv
nsteps   = 1000
dt   = 0.002
constraints  = all-bonds
constraint-algorithm = shake
nstcomm  = 1
nstcalcenergy= 1
ns_type  = grid
rlist= 1.3
rcoulomb = 1.3
rvdw = 1.3
vdwtype  = cut-off
coulombtype  = PME
Tcoupl   = Andersen
nsttcouple   = 1
tau_t= 0.1
tc-grps  = system
ref_t= 300
Pcoupl   = mttk
Pcoupltype   = isotropic
nstpcouple   = 1
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
gen_vel  = yes
nstxout  = 2 ; write coords every # step
lincs-iter   = 2
DispCorr = EnerPres
optimize_fft = yes
EOF

wget -c "http://www.pdbe.org/download/1brv";; -O 1brv.pdb

pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh

editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0

genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs

grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr

echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p
Prot.top -norandom

grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr

mdrun -v -deffnm em

grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr

mdrun-gpu -v -deffnm md -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"

---
Getting Loaded...
Reading file md.tpr, VERSION 4.5 (single precision)

---
Program mdrun-gpu, VERSION 4.5-GPU-beta2
Source code file:
/home/rossen/Research/Projects/Gromacs-dev/gromacs/src/gmxlib/tpxio.c,
line: 1971

Fatal error:
reading tpx file (md.tpr) version 73 with version 71 program
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

I also have tried to use my own system to test the mdrun-gpu and I got
the same error.
Any ideas?

Thanks,

Renato
-- 
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