[gmx-users] REMD error

[bharat gupta]

Hi,

I am trying to run a REMD of a peptide. But while executing the following
command after nvt and npt equilibration , I am getting the following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission denied


Can anybody suggest me how could I rectify this error.

-- 
Bharat
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[gmx-users] REMD Error

[Jose Tusell]

I know this error has been reported before and Mark Abraham suggested to
file a bug report on redmine.  While starting regular NPT remd on my system
I run into the following problem:

init_step+nsteps is not equal for all subsystems
  subsystem 0: 2500
  subsystem 1: 0
  subsystem 2: 2500
  subsystem 3: 0
  subsystem 4: 2500
  subsystem 5: 0
  subsystem 6: 2500
  subsystem 7: 0
  subsystem 8: 2500
  subsystem 9: 0
  subsystem 10: 2500
  subsystem 11: 0
  subsystem 12: 2500

---
Program mdrun_mpi_d, VERSION 4.5.4
Source code file: main.c, line: 249

Fatal error:
The 64 subsystems are not compatible

gmxdump gives the same nsteps and init_step.  Let me know what you'd need to
file a bug on redmine.

Thanks,

Jose Tusell
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Re: [gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 11:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while executing the 
following command after nvt and npt equilibration , I am getting the 
following error:-


mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: 
cannot enable executable stack as shared object requires: Permission 
denied




You configured GROMACS to use shared libraries, but something about them 
or your current environment doesn't work. Try rebuilding GROMACS, 
building with static libraries, or discussing with your system admins.


Mark
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Re: [gmx-users] REMD error

[lina]

On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means system does 
not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat



--
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Re: [gmx-users] REMD error

[bharat gupta]

Thanks for the advice I re-complied everything again with static libraries
and the installation went fine. But while executing the following command I
am again getting error :-


mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .



On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:

> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>
>> Hi,
>>
>> I am trying to run a REMD of a peptide. But while executing the
>> following command after nvt and npt equilibration , I am getting the
>> following error:-
>>
>> mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
>> mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
>> enable executable stack as shared object requires: Permission denied
>>
>
> Can you run a normal md smoothly?
> try:
> mdrun_mpi mdrun -deffnm prefix_0
>
> if it works, then some of your trajectories not sound. means system does
> not equilibrium well.
>
>
>>
>> Can anybody suggest me how could I rectify this error.
>>
>> --
>> Bharat
>>
>>
> --
> 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/Searchbefore
>  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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 5:29 PM, bharat gupta wrote:
Thanks for the advice I re-complied everything again with static 
libraries and the installation went fine. But while executing the 
following command I am again getting error :-



mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (3)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .


See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps 
point 2. You cannot simulate an arbitrary number of replicas on an 
arbitrary number of processors.


Mark





On Thu, Jan 12, 2012 at 1:37 PM, lina > wrote:


On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am
getting the
following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries:
libgmx_mpi.so.6: cannot
enable executable stack as shared object requires: Permission
denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means
system does not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat


-- 
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 





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Re: [gmx-users] REMD error

[bharat gupta]

It says that "The number of cores must be a multiple of the number of
replicas (given with -multi, which must equal the number of
.tprfiles
i.e., 10 for the above general example using
prefix_0.tpr through prefix_9.tpr)"

I gave the options -multi 5 . But still I am getting the same error. Can
you please explain, why is it so. Do I need to have the same no. of cores
as the no. of .tpr files ??

On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham wrote:

>  On 12/01/2012 5:29 PM, bharat gupta wrote:
>
> Thanks for the advice I re-complied everything again with static libraries
> and the installation went fine. But while executing the following command I
> am again getting error :-
>
>
> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>
>
> Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (3)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> Halting program mdrun_mpi
>
> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>
>
> I am trying to simulate 5 replicas and I have 4 cpu .
>
>
> See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
> point 2. You cannot simulate an arbitrary number of replicas on an
> arbitrary number of processors.
>
> Mark
>
>
>
>
>
> On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:
>
>> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>>
>>> Hi,
>>>
>>> I am trying to run a REMD of a peptide. But while executing the
>>> following command after nvt and npt equilibration , I am getting the
>>> following error:-
>>>
>>> mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
>>> mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
>>> enable executable stack as shared object requires: Permission denied
>>>
>>
>>  Can you run a normal md smoothly?
>> try:
>> mdrun_mpi mdrun -deffnm prefix_0
>>
>> if it works, then some of your trajectories not sound. means system does
>> not equilibrium well.
>>
>>
>>>
>>> Can anybody suggest me how could I rectify this error.
>>>
>>> --
>>> Bharat
>>>
>>>
>>   --
>> 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
>>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com
>
>
>
>
>
> --
> 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
>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
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Re: [gmx-users] REMD error

[Mark Abraham]

On 12/01/2012 5:45 PM, bharat gupta wrote:
It says that "The number of cores must be a multiple of the number of 
replicas (given with |-multi|, which must equal the number of .tpr 
 
files i.e., 10 for the above general example using |prefix_0.tpr| 
through |prefix_9.tpr|)"


I gave the options -multi 5 . But still I am getting the same error. 
Can you please explain, why is it so. Do I need to have the same no. 
of cores as the no. of .tpr files ??


You can't be getting an identical error, the numbers are different now.

If mdrun is reporting the number of nodes is 1, then you have not 
configured your MPI environment correctly so that it knows how many 
processors you have available. You will need to solve this by reading 
your MPI documentation.


If you have only four processors, you will not be able to run efficient 
REMD on five replicas, even if you can work out how to get MPI to 
over-allocate MPI processes to your physical processors.


Please copy and paste command line and error together, so that people 
who might help don't feel like they might be wasting their time 
guessing. They have other things to do. Your example input below did not 
produce your error below, because 20 != 3.


Mark



On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham > wrote:


On 12/01/2012 5:29 PM, bharat gupta wrote:

Thanks for the advice I re-complied everything again with static
libraries and the installation went fine. But while executing the
following command I am again getting error :-


mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v


Fatal error:
The number of nodes (1) is not a multiple of the number of
simulations (3)
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)

Halting program mdrun_mpi

gcq#155: "BioBeat is Not Available In Regular Shops" (P.J.
Meulenhoff)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


I am trying to simulate 5 replicas and I have 4 cpu .


See http://www.gromacs.org/Documentation/How-tos/REMD Execution
Steps point 2. You cannot simulate an arbitrary number of replicas
on an arbitrary number of processors.

Mark






On Thu, Jan 12, 2012 at 1:37 PM, lina mailto:lina.lastn...@gmail.com>> wrote:

On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:

Hi,

I am trying to run a REMD of a peptide. But while
executing the
following command after nvt and npt equilibration , I am
getting the
following error:-

mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while loading shared libraries:
libgmx_mpi.so.6: cannot
enable executable stack as shared object requires:
Permission denied


Can you run a normal md smoothly?
try:
mdrun_mpi mdrun -deffnm prefix_0

if it works, then some of your trajectories not sound. means
system does not equilibrium well.



Can anybody suggest me how could I rectify this error.

--
Bharat


-- 
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
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-- 
Bharat

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 






--
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering an

Re: [gmx-users] REMD error

[bharat gupta]

The command I used this time :-

mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100


Here's the error that I got :-

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Look at these, my work-strong arms" (P.J. Harvey)

Halting program mdrun_mpi

gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0


On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham wrote:

>  On 12/01/2012 5:45 PM, bharat gupta wrote:
>
> It says that "The number of cores must be a multiple of the number of
> replicas (given with -multi, which must equal the number of 
> .tprfiles
>  i.e., 10 for the above general example using
> prefix_0.tpr through prefix_9.tpr)"
>
> I gave the options -multi 5 . But still I am getting the same error. Can
> you please explain, why is it so. Do I need to have the same no. of cores
> as the no. of .tpr files ??
>
>
> You can't be getting an identical error, the numbers are different now.
>
> If mdrun is reporting the number of nodes is 1, then you have not
> configured your MPI environment correctly so that it knows how many
> processors you have available. You will need to solve this by reading your
> MPI documentation.
>
> If you have only four processors, you will not be able to run efficient
> REMD on five replicas, even if you can work out how to get MPI to
> over-allocate MPI processes to your physical processors.
>
> Please copy and paste command line and error together, so that people who
> might help don't feel like they might be wasting their time guessing. They
> have other things to do. Your example input below did not produce your
> error below, because 20 != 3.
>
>
> Mark
>
>
> On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham wrote:
>
>>  On 12/01/2012 5:29 PM, bharat gupta wrote:
>>
>> Thanks for the advice I re-complied everything again with static
>> libraries and the installation went fine. But while executing the following
>> command I am again getting error :-
>>
>>
>> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>>
>>
>> Fatal error:
>> The number of nodes (1) is not a multiple of the number of simulations (3)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> ---
>>
>> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>>
>> Halting program mdrun_mpi
>>
>> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>>
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>>
>>
>> I am trying to simulate 5 replicas and I have 4 cpu .
>>
>>
>>  See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
>> point 2. You cannot simulate an arbitrary number of replicas on an
>> arbitrary number of processors.
>>
>> Mark
>>
>>
>>
>>
>>
>> On Thu, Jan 12, 2012 at 1:37 PM, lina  wrote:
>>
>>> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>>>
 Hi,

 I am trying to run a REMD of a peptide. But while executing the
 following command after nvt and npt equilibration , I am getting the
 following error:-

 mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
 mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
 enable executable stack as shared object requires: Permission denied

>>>
>>>  Can you run a normal md smoothly?
>>> try:
>>> mdrun_mpi mdrun -deffnm prefix_0
>>>
>>> if it works, then some of your trajectories not sound. means system does
>>> not equilibrium well.
>>>
>>>

 Can anybody suggest me how could I rectify this error.

 --
 Bharat


>>>   --
>>> 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
>>>
>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46...@yahoo.com
>>
>>
>>
>>
>>
>> --
>> 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 po

Re: [gmx-users] REMD Error

[Mark Abraham]

On 3/09/2011 3:08 PM, Jose Tusell wrote:
I know this error has been reported before and Mark Abraham suggested 
to file a bug report on redmine.  While starting regular NPT remd on 
my system I run into the following problem:


init_step+nsteps is not equal for all subsystems
  subsystem 0: 2500
  subsystem 1: 0
  subsystem 2: 2500
  subsystem 3: 0
  subsystem 4: 2500
  subsystem 5: 0
  subsystem 6: 2500
  subsystem 7: 0
  subsystem 8: 2500
  subsystem 9: 0
  subsystem 10: 2500
  subsystem 11: 0
  subsystem 12: 2500

---
Program mdrun_mpi_d, VERSION 4.5.4
Source code file: main.c, line: 249

Fatal error:
The 64 subsystems are not compatible

gmxdump gives the same nsteps and init_step.  Let me know what you'd 
need to file a bug on redmine.


A description of how to reproduce the problem, GROMACS version and input 
files to re-create the problem in a short run. Assuming you're not 
deliberately providing mismatching .tpr files, the question becomes how 
init_step + nsteps becomes different for the different .tpr files. That 
seems to be during grompp, since gmxdump agrees on the contents of the 
.tpr files.


Mark
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Re: [gmx-users] REMD Error

[Jose Tusell]

Mark,

I've check the *.tpr files for inconsistencies in steps and init_step and
found that they are both the same.  I'll file a bug report in redmine and
I'll attach all the necessary information about the initial setup.

Jose R Tusell

On Fri, Sep 2, 2011 at 11:55 PM, Mark Abraham wrote:

> On 3/09/2011 3:08 PM, Jose Tusell wrote:
>
>> I know this error has been reported before and Mark Abraham suggested to
>> file a bug report on redmine.  While starting regular NPT remd on my system
>> I run into the following problem:
>>
>> init_step+nsteps is not equal for all subsystems
>>  subsystem 0: 2500
>>  subsystem 1: 0
>>  subsystem 2: 2500
>>  subsystem 3: 0
>>  subsystem 4: 2500
>>  subsystem 5: 0
>>  subsystem 6: 2500
>>  subsystem 7: 0
>>  subsystem 8: 2500
>>  subsystem 9: 0
>>  subsystem 10: 2500
>>  subsystem 11: 0
>>  subsystem 12: 2500
>>
>> --**-
>> Program mdrun_mpi_d, VERSION 4.5.4
>> Source code file: main.c, line: 249
>>
>> Fatal error:
>> The 64 subsystems are not compatible
>>
>> gmxdump gives the same nsteps and init_step.  Let me know what you'd need
>> to file a bug on redmine.
>>
>
> A description of how to reproduce the problem, GROMACS version and input
> files to re-create the problem in a short run. Assuming you're not
> deliberately providing mismatching .tpr files, the question becomes how
> init_step + nsteps becomes different for the different .tpr files. That
> seems to be during grompp, since gmxdump agrees on the contents of the .tpr
> files.
>
> Mark
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Re: [gmx-users] REMD Error

[Jose Tusell]

Hi Mark,

I just posted a bug on redmine for the remd problem that I encountered.  I
was as thorough as possible about how to recreate the bug, but if I forgot
some crucial piece of information let me know and I will get it to you as
soon as possible.  Thanks for your time.

Jose Tusell

On Sat, Sep 3, 2011 at 9:41 AM, Jose Tusell  wrote:

> Mark,
>
> I've check the *.tpr files for inconsistencies in steps and init_step and
> found that they are both the same.  I'll file a bug report in redmine and
> I'll attach all the necessary information about the initial setup.
>
> Jose R Tusell
>
>
> On Fri, Sep 2, 2011 at 11:55 PM, Mark Abraham wrote:
>
>> On 3/09/2011 3:08 PM, Jose Tusell wrote:
>>
>>> I know this error has been reported before and Mark Abraham suggested to
>>> file a bug report on redmine.  While starting regular NPT remd on my system
>>> I run into the following problem:
>>>
>>> init_step+nsteps is not equal for all subsystems
>>>  subsystem 0: 2500
>>>  subsystem 1: 0
>>>  subsystem 2: 2500
>>>  subsystem 3: 0
>>>  subsystem 4: 2500
>>>  subsystem 5: 0
>>>  subsystem 6: 2500
>>>  subsystem 7: 0
>>>  subsystem 8: 2500
>>>  subsystem 9: 0
>>>  subsystem 10: 2500
>>>  subsystem 11: 0
>>>  subsystem 12: 2500
>>>
>>> --**-
>>> Program mdrun_mpi_d, VERSION 4.5.4
>>> Source code file: main.c, line: 249
>>>
>>> Fatal error:
>>> The 64 subsystems are not compatible
>>>
>>> gmxdump gives the same nsteps and init_step.  Let me know what you'd need
>>> to file a bug on redmine.
>>>
>>
>> A description of how to reproduce the problem, GROMACS version and input
>> files to re-create the problem in a short run. Assuming you're not
>> deliberately providing mismatching .tpr files, the question becomes how
>> init_step + nsteps becomes different for the different .tpr files. That
>> seems to be during grompp, since gmxdump agrees on the contents of the .tpr
>> files.
>>
>> Mark
>> --
>> 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/Searchbefore
>>  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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