bre 2011 14:40:39
Oggetto: Re: [gmx-users] segmentation fault from power6 kernel
On 3/11/2011 7:59 PM, Fabio Affinito wrote:
Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.
Sounds like a bug. Pleas
;t know
why the usual error messages in such scenarios did not arise on this
platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to
1 to see if this is a power6-specific kernel issue. Try running the .tpr
on another platform.
Mark
--
Fabio Affinito, PhD
SuperComputing Applications
Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with
TotalView and I've found that this segmentation violation originates in the
pwr6kernel310.F
Up to now, I still didn't find what is behind this s
Ok, the problem is solved.
Thank you.
Fabio
On 07/27/2011 05:17 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Thanks.
This actually solved the problem in grompp.
I still have problems when running. This is the log of mdrun:
Initializing Domain Decomposition on 4096 nodes
Dynamic load
s and rcon parameter. Am I right?
Fabio
On 07/27/2011 04:48 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the key part:
processing coordinates...
Warning: atom name 18113 in topol.top and out.gro does not match (MN1
- CN1)
Warning: atom name 18114 in topol.top and out.gro does
On 07/27/2011 04:12 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain
On 07/27/2011 03:54 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
This is the mdrun output:
Initializing Domain Decomposition on 4096 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body
On 07/27/2011 03:38 PM, Justin A. Lemkul wrote:
Please make sure to keep the discussion on the list.
Sorry, I just was continuing the discussion after sending you my
coordinates.
Fabio Affinito wrote:
Justin,
first of all, I thank you very much for your help: it's very precio
On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021
On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
Maybe this is a different issue... but it's ok that after the 99,999th
atom the counter restarts from zero?
21374SOL OW9 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0
oblem?
Thanks again,
Fabio
On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If
not,
the
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
Fabio Affinito wrote:
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
Were the molecules whole in the coordinate file you replicated? If not,
the bonds will now be assigned across the entire box.
-Justin
Yes and not, depending on what you
ur chains.
This clarifies? (i guess not..)
F
--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794 Fax: +39 051 6132198
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http://li
n you give me some suggestions?
Thanks in advance,
Fabio
--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794 Fax: +39 051 6132198
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ns -np 256 -s md_.tpr -multi 8
>> -replex 1000
>> >
>> >
>> >There have been two threads on this topic in the last month or so,
>> please check the archives. The implementation of
>> >multi-simulations scales poorly. The scaling of replica-exchange
>
drun_mpi_bg_d on CPU 188 out of 256
>
Can anybody give me some hint about that?
Thanks in advance,
Fabio
--
*
Fabio Affinito, PhD
CINECA
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bol
cin0644a/gromacs-4.5.3/src/kernel'
The directory /lib:
> libfftw.a libfftw_threads.a librfftw.a librfftw_threads.a
> libfftw.la libfftw_threads.la librfftw.la librfftw_threads.la
The directory /include:
> fftw.h fftw_threads.h rfftw.h rfftw_threads.h
Do you have any hint
t; libfftw.la libfftw_threads.la librfftw.la
>> librfftw_threads.la
>> The directory /include:
>>
>> > fftw.h fftw_threads.h rfftw.h rfftw_threads.h
>>
>> Do you have any hint?
>
> I'd be looking for errors higher up in the output, where
> mdlib/libmd_mpi.la got (not) made.
>
> Mar
ter the 50% of the structures, and also in this case the cutoff
> would be different for the different cases...
>
> Any hint?
> Thanks a lot,
> Valeria
>
>
>
Option ii) is the right one.
Fabio
--
*
Fabio Affinito, PhD
CINE
l Message -
> From: Fabio Affinito
> Date: Thursday, September 23, 2010 20:54
> Subject: Re: [gmx-users] ffyw3f library not found..
> To: Discussion list for GROMACS users
>
>> On 09/23/2010 12:27 PM, Kamalesh Roy wrote:
>> > Dear users
>> >
>> > I am tr
S="-L/bgp/userinternal/cin0644a/fftwlibs/lib"
This is my error in 4.5.1
checking for sqrt in -lm... yes
checking for fftw3.h... yes
checking for main in -lfftw3f... no
configure: error: Cannot find fftw3f library
Whilst in 4.0.7 everything works.
Any hints?
Thanks in advance,
Fabi
\
FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \
LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib"
is fine with 4.0.7 but it generates
checking for main in -lfftw3f... no
configure: error: Cannot find fftw3f library
in 4.5.1
I successfully
Like for the frontend, the --enable-fortran is the problem.
Maybe it could be useful to update the instruction page :)
Fabio
On 09/21/2010 10:54 AM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Fabio Affinito
> Date: Tuesday, September 21, 2010 18:51
>
;> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_ker
f77_single/nb_kernel_f77_single.c",
> line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single.
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",
> line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single.
> "../../.
116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single.
"../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",
line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single.
Do you have any hint about that?
Thanks in advance!
F.
--
Peyman,
the protein moves because the c.o.m. motion wasn't subtracted during
the dynamics.
On Tuesday 01 July 2008 12:24, Fabio Affinito wrote:
I think if it moves, then there is something more basic wrong, do
you remove
your center of mass motion appropriately? is you
I choosed "Protein" for centering and "System" for output.
Same stuff with editconf.
F.
Fabio Affinito, PhD
email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528
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The protein experience self-diffusion and so it moves through the
simulation box.
I tried also with editconf but the result is the same.
F.
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Please
Hi all,
During my MD the molecule experience a drift. Now I want to put the
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and using a
reference frame where the molecule is at the center of the box.
It seems that all the box (water+molecule) i
Hi Berk,
thanks for your answer. I've checked the charge groups and every thing
seems to be ok (no single groups...). Actually I'm using 3.2.1
version, but it doesn't seem to be depending on that.
What could I check?
Fabio
On May 8, 2008, at 4:00 PM, [EMAIL PROTECTED] wrote:
-
Dear all,
During my simulations of a GFP protein (force field made with amber,
then converted to gromacs), I usually get this error:
Fatal error: ci = 8108 should be in 0 .. 7937 [FILE nsgrid.c, LINE 218]
What this that means?
If I restart the simulation from the frame just before the crash
I've been running on 16 processors a protein MD simulation. During the
simulation I've got a crash and the standard error reported this:
Fatal error: ci = 10280 should be in 0 .. 10050 [FILE nsgrid.c, LINE 218]
[0] MPI Abort by user Aborting program !
[0] Aborting program!
What could that be?
post? Read http://www.gromacs.org/mailing_lists/users.php
Fabio Affinito, PhD
SISSA/ISAS - Statistical and Biological Physics
Via Beirut, 4 email: [EMAIL PROTECTED]
34014 Trieste phone: +39 040
Dear all,
Using
g_angle -f ../trj1_0_100.xtc -s ../g_prot.tpr -n test.ndx -or -type
dihedral -e 1
As expected, I obtained the following statement
[cut]
Group 0 (Backbone) has 664 elements
There is one group in the index
Reading file ../g_prot.tpr, VERSION 3.2.1 (single precisio
angle multiplicity force constant
so, does it refer to the angle values contained in the topology files?
Thank you,
Fabio
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Please search the archive
Hi everybody,
what's the meaning of the labels in the angle.ndx generated by the
mk_angndx?
For example, I've got groups named [ Phi=0.0_3_3.77 ]..
what does that mean?
Thanks,
Fabio
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