Re: [gmx-users] gmxtest failures OK?

2009-08-28 Thread Warren Gallin 

I could only find the 4.0.4 tests, which are what I ran.

Where would I find the latest tests?

Warren Gallin

On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote:



Which test set are you using?  These failures are to be expected for  
earlier versions in the 4.0.x series, but were fixed in a 4.0.5- 
compatible version.  I don't believe these failures ever indicated  
anything truly wrong, but the newest version has different (clearer  
and more detailed) output and all the tests should pass.


-Justin

Warren Gallin wrote:

Hi,
   I just installed v. 4.0.5
   Wen I ran the gmxtests I got the following output:
All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED
Am I correct in thinking that these kernel failures are expected,  
and therefore that the installation worked?

Thanks,
Warren Gallin
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ICTAS Doctoral Scholar
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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Re: [gmx-users] gmxtest failures OK?

2009-08-28 Thread Justin A. Lemkul 



Warren Gallin wrote:

I could only find the 4.0.4 tests, which are what I ran.

Where would I find the latest tests?



It used to be linked from the wiki, but the site is still down and I can't find 
it on the main page.  I imagine you could pull down the latest development 
version (which should have all the 4.0.5-relevant changes implemented) from the 
git repository.  Instructions are here:


http://www.gromacs.org/Developers/Git/Basic_Git_Usage

-Justin


Warren Gallin

On 28-Aug-09, at 3:42 PM, Justin A. Lemkul wrote:



Which test set are you using?  These failures are to be expected for 
earlier versions in the 4.0.x series, but were fixed in a 
4.0.5-compatible version.  I don't believe these failures ever 
indicated anything truly wrong, but the newest version has different 
(clearer and more detailed) output and all the tests should pass.


-Justin

Warren Gallin wrote:

Hi,
   I just installed v. 4.0.5
   Wen I ran the gmxtests I got the following output:
All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED
Am I correct in thinking that these kernel failures are expected, and 
therefore that the installation worked?

Thanks,
Warren Gallin
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Re: [gmx-users] gmxtest failures OK?

2009-08-28 Thread Justin A. Lemkul 


Which test set are you using?  These failures are to be expected for earlier 
versions in the 4.0.x series, but were fixed in a 4.0.5-compatible version.  I 
don't believe these failures ever indicated anything truly wrong, but the newest 
version has different (clearer and more detailed) output and all the tests 
should pass.


-Justin

Warren Gallin wrote:

Hi,

I just installed v. 4.0.5

Wen I ran the gmxtests I got the following output:


All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED


Am I correct in thinking that these kernel failures are expected, and 
therefore that the installation worked?


Thanks,

Warren Gallin

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] gmxtest failures OK?

2009-08-28 Thread Warren Gallin 

Hi,

I just installed v. 4.0.5

Wen I ran the gmxtests I got the following output:


All 16 simple tests PASSED
All 14 complex tests PASSED
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
All 45 pdb2gmx tests PASSED


Am I correct in thinking that these kernel failures are expected, and  
therefore that the installation worked?


Thanks,

Warren Gallin

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Re: [gmx-users] gmxtest

2009-06-11 Thread Justin A. Lemkul 



Jones de Andrade wrote:

Hi all.

Sorry for waking up this subject again. But it rise a question for me:

Is gmx 4 or gmx 3.3 that has a bug so?

And, what is the bug concerned exactly? Buckingham interaction, 1-4 
interactions, or buckingham 1-4 interactions?




http://bugzilla.gromacs.org/show_bug.cgi?id=313

Version 3.3 had the bug, related to Buckingham interactions.  The full 
explanation is in the bug report/resolution.


-Justin


Thanks a lot in advance,

Sincerally yours,

Jones

On Wed, May 27, 2009 at 1:03 AM, Mark Abraham > wrote:


Mark Abraham wrote:

Simba Xiao wrote:

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p,
ti4pflex and some kernel issues failed.


That's normal at the moment, unfortunately. Future releases of
gmxtest will probably fix the non-kernel issues, and GROMACS >
4.0.5 will fix the kernel issues.


Sorry, I mis-remembered something. The kernel issues were caused by
a hard-to-provoke bug in 3.3.x which provided the reference
trajectories. GROMACS 4.0.x are fine, but the test fails because of
the flawed reference values. See bugzilla 313 for details.

Mark


I use standard packages and everything looks find. The
simulation result are good and identical  to gromacs 3.3.3.

But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody
tell something more than the wiki tells (It dose not explain
much).


Well, it does explain things, but not such that a new GROMACS
user can get a useful result from existing versions of gmxtest.
I'll upgrade the wiki documentation if/when a gmxtest re-release
happens.

Mark
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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Re: [gmx-users] gmxtest

2009-06-11 Thread Jones de Andrade 
Hi all.

Sorry for waking up this subject again. But it rise a question for me:

Is gmx 4 or gmx 3.3 that has a bug so?

And, what is the bug concerned exactly? Buckingham interaction, 1-4
interactions, or buckingham 1-4 interactions?

Thanks a lot in advance,

Sincerally yours,

Jones

On Wed, May 27, 2009 at 1:03 AM, Mark Abraham wrote:

> Mark Abraham wrote:
>
>> Simba Xiao wrote:
>>
>>> Dear all,
>>>
>>> Does your GMX 4 past the gmxtest package in the gmx wiki ?
>>>
>>> My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex and
>>> some kernel issues failed.
>>>
>>
>> That's normal at the moment, unfortunately. Future releases of gmxtest
>> will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix the
>> kernel issues.
>>
>
> Sorry, I mis-remembered something. The kernel issues were caused by a
> hard-to-provoke bug in 3.3.x which provided the reference trajectories.
> GROMACS 4.0.x are fine, but the test fails because of the flawed reference
> values. See bugzilla 313 for details.
>
> Mark
>
>
>  I use standard packages and everything looks find. The simulation result
>>> are good and identical  to gromacs 3.3.3.
>>>
>>> But, still it annoys me with the test result.
>>>
>>> Can somebody tell how much the test matters and can somebody tell
>>> something more than the wiki tells (It dose not explain much).
>>>
>>
>> Well, it does explain things, but not such that a new GROMACS user can get
>> a useful result from existing versions of gmxtest. I'll upgrade the wiki
>> documentation if/when a gmxtest re-release happens.
>>
>> Mark
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Re: [gmx-users] gmxtest

2009-05-27 Thread Simba Xiao 
Hi Mark,

Thanks!
S.


On Wed, May 27, 2009 at 12:03 PM, Mark Abraham wrote:

> Mark Abraham wrote:
>
>> Simba Xiao wrote:
>>
>>> Dear all,
>>>
>>> Does your GMX 4 past the gmxtest package in the gmx wiki ?
>>>
>>> My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex and
>>> some kernel issues failed.
>>>
>>
>> That's normal at the moment, unfortunately. Future releases of gmxtest
>> will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix the
>> kernel issues.
>>
>
> Sorry, I mis-remembered something. The kernel issues were caused by a
> hard-to-provoke bug in 3.3.x which provided the reference trajectories.
> GROMACS 4.0.x are fine, but the test fails because of the flawed reference
> values. See bugzilla 313 for details.
>
> Mark
>
>
>  I use standard packages and everything looks find. The simulation result
>>> are good and identical  to gromacs 3.3.3.
>>>
>>> But, still it annoys me with the test result.
>>>
>>> Can somebody tell how much the test matters and can somebody tell
>>> something more than the wiki tells (It dose not explain much).
>>>
>>
>> Well, it does explain things, but not such that a new GROMACS user can get
>> a useful result from existing versions of gmxtest. I'll upgrade the wiki
>> documentation if/when a gmxtest re-release happens.
>>
>> Mark
>> ___
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
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-- 
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CHINA
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Re: [gmx-users] gmxtest

2009-05-26 Thread Mark Abraham 

Mark Abraham wrote:

Simba Xiao wrote:

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex 
and some kernel issues failed.


That's normal at the moment, unfortunately. Future releases of gmxtest 
will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix 
the kernel issues.


Sorry, I mis-remembered something. The kernel issues were caused by a 
hard-to-provoke bug in 3.3.x which provided the reference trajectories. 
GROMACS 4.0.x are fine, but the test fails because of the flawed 
reference values. See bugzilla 313 for details.


Mark

I use standard packages and everything looks find. The simulation 
result are good and identical  to gromacs 3.3.3.


But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell 
something more than the wiki tells (It dose not explain much).


Well, it does explain things, but not such that a new GROMACS user can 
get a useful result from existing versions of gmxtest. I'll upgrade the 
wiki documentation if/when a gmxtest re-release happens.


Mark
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Re: [gmx-users] gmxtest

2009-05-26 Thread Mark Abraham 

Simba Xiao wrote:

Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex 
and some kernel issues failed.


That's normal at the moment, unfortunately. Future releases of gmxtest 
will probably fix the non-kernel issues, and GROMACS > 4.0.5 will fix 
the kernel issues.


I use standard packages and everything looks find. The simulation result 
are good and identical  to gromacs 3.3.3.


But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell 
something more than the wiki tells (It dose not explain much).


Well, it does explain things, but not such that a new GROMACS user can 
get a useful result from existing versions of gmxtest. I'll upgrade the 
wiki documentation if/when a gmxtest re-release happens.


Mark
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[gmx-users] gmxtest

2009-05-26 Thread Simba Xiao 
Dear all,

Does your GMX 4 past the gmxtest package in the gmx wiki ?

My Gromacs 4.0.4 can not pass all the test. The test  tip4p, ti4pflex and
some kernel issues failed.

I use standard packages and everything looks find. The simulation result are
good and identical  to gromacs 3.3.3.

But, still it annoys me with the test result.

Can somebody tell how much the test matters and can somebody tell something
more than the wiki tells (It dose not explain much).

Great thanks!
S.

--
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[gmx-users] gmxtest error: Only 44 energies in the log file

2008-11-17 Thread DimitryASuplatov 
Hello,
I`ve been using gromacs 4 since the release and have experienced no
problems or artifacts during simulations. When I ran gmxtest-3.3.3
(./gmxtest.pl all) I`ve received the following error message:

= START =
All 16 simple tests PASSED
All 14 complex tests PASSED
All 63 kernel tests PASSED
Error not all 45 pdb2gmx tests have been done successfully
Only 44 energies in the log file
== END ==

I`ve then upgraded to gromacs 4.0.2 with intell icc and ifort v11.0.69
and intel mpi v3.2 (openSuSE 11.0). I`ve the same error.

pdb2gmx log file is 1.3 MB file so I can not attach it here. 
I think it might be something wrong with the gmxtest script of v3.3.3 in
the first place because errors from the log look like "file not found",
"atom type not found" etc.
Do you have any suggestions? Thanks.
SDA

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Re: [gmx-users] gmxtest rb1

2008-10-15 Thread Juliana Angeiras 
Hi,
 
I will to upgrade to 4.0
Thanks,
 
Juliana.

--- Em qua, 15/10/08, David van der Spoel <[EMAIL PROTECTED]> escreveu:

De: David van der Spoel <[EMAIL PROTECTED]>
Assunto: Re: [gmx-users] gmxtest rb1
Para: "Discussion list for GROMACS users" 
Data: Quarta-feira, 15 de Outubro de 2008, 6:10

Juliana Angeiras wrote:
> 
> Hi all,
>  
> I'm still having problems with the simple test in the directory rb1. I

> have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the 
> directory simple/rb1/ crashed. The complex test dec+water too, but the 
> problem seems not too serious as the related in the wiki. The 
> configuration and the output are below.
>  

Hi Juliana,

I have reproduced this bug. It has been fixed in the most recent CVS but 
not in the 3.3.3 tree. A fix will be in release 4.0.1. I willhave a 
quick look to see whether it is easy to port the fixes to 3.3 (although 
we would like everyone to upgrade to 4.0).


> Thanks,
>  
> Juliana.
> 
>  > I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some
>  > problems when i had ran the gmxtest. The output is posted below:
>  > ./gmxtest.pl all
>  > *** glibc detected *** mdrun: realloc(): invalid next size: 
> 0x09e070d0 ***
>  > === Backtrace: =
>  > /lib/libc.so.6[0xb0d440]
>  > /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
>  > mdrun[0x8136675]
>  > === Memory map: 
>  > 00101000-0020 r-xp  fd:00 250620
/usr/lib/libX11.so.6.2.0
>  > 0020-00204000 rwxp 000ff000 fd:00 250620
/usr/lib/libX11.so.6.2.0
>  > 00204000-00205000 rwxp 00204000 00:00 0
>  > 002bf000-002c rwxp 002bf000 00:00 0
>  > 004c7000-004c8000 rwxp 004c7000 00:00 0
>  > 00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
>  > 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
>  > 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
>  > 0084a000-0084c000 rwxp 0084a000 00:00 0
>  > 008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
>  > 008bf000-008c rwxp 008bf000 00:00 0
>  > 009e8000-009f r-xp  fd:00 250635
/usr/lib/libSM.so.6.0.0
>  > 009f-009f1000 rwxp 7000 fd:00 250635
/usr/lib/libSM.so.6.0.0
>  > 009fa000-00a11000 r-xp  fd:00 250634
/usr/lib/libICE.so.6.3.0
>  > 00a11000-00a12000 rwxp 00016000 fd:00 250634
/usr/lib/libICE.so.6.3.0
>  > 00a12000-00a14000 rwxp 00a12000 00:00 0
>  > 00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
>  > 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
>  > 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
>  > 00a9d000-00a9f000 r-xp  fd:00 250618
/usr/lib/libXau.so.6.0.0
>  > 00a9f000-00aa rwxp 1000 fd:00 250618
/usr/lib/libXau.so.6.0.0
>  > 00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
>  > 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
>  > 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
>  > 00be2000-00be5000 rwxp 00be2000 00:00 0
>  > 00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
>  > 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
>  > 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
>  > 00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
>  > 00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
>  > 00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
>  > 00d3-00d35000 r-xp  fd:00 250619   
> /usr/lib/libXdmcp.so.6.0.0
>  > 00d35000-00d36000 rwxp 4000 fd:00 250619   
> /usr/lib/libXdmcp.so.6.0.0
>  > 049e1000-049ec000 r-xp  fd:00 197087
>  > /lib/libgcc_s-4.1.2-20080102.so.1
>  > 049ec000-049ed000 rwxp a000 fd:00 197087
>  > /lib/libgcc_s-4.1.2-20080102.so.1
>  > 08048000-082f8000 r-xp  fd:00 1104196   
>  > /usr/local/gromacs/bin/mdrun
>  > 082f8000-082ff000 rwxp 002b fd:00 1104196   
>  > /usr/local/gromacs/bin/mdrun
>  > 082ff000-08304000 rwxp 082ff000 00:00 0
>  > 09df4000-09e15000 rwxp 09df4000 00:00 0
>  > b7e0-b7e21000 rwxp b7e0 00:00 0
>  > b7e21000-b7f0 --xp b7e21000 00:00 0
>  > bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
>  > sh: line 1: 17103 Abortadomdrun > mdrun.out
2>&1
>  > FAILED. Check files in rb1
>  > 1 out of 16 simple tests FAILED
>  > FAILED. Check files in dec+water
>  > 1 out of 14 complex tests FAILED
>  > All 63 kernel tests PASSED
>  > All 45 pdb2gmx tests PASSED
>  > I have tried install the gr

Re: [gmx-users] gmxtest rb1

2008-10-15 Thread David van der Spoel 

Juliana Angeiras wrote:


Hi all,
 
I'm still having problems with the simple test in the directory rb1. I 
have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the 
directory simple/rb1/ crashed. The complex test dec+water too, but the 
problem seems not too serious as the related in the wiki. The 
configuration and the output are below.
 


Hi Juliana,

I have reproduced this bug. It has been fixed in the most recent CVS but 
not in the 3.3.3 tree. A fix will be in release 4.0.1. I willhave a 
quick look to see whether it is easy to port the fixes to 3.3 (although 
we would like everyone to upgrade to 4.0).




Thanks,
 
Juliana.


 > I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some
 > problems when i had ran the gmxtest. The output is posted below:
 > ./gmxtest.pl all
 > *** glibc detected *** mdrun: realloc(): invalid next size: 
0x09e070d0 ***

 > === Backtrace: =
 > /lib/libc.so.6[0xb0d440]
 > /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
 > mdrun[0x8136675]
 > === Memory map: 
 > 00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
 > 0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
 > 00204000-00205000 rwxp 00204000 00:00 0
 > 002bf000-002c rwxp 002bf000 00:00 0
 > 004c7000-004c8000 rwxp 004c7000 00:00 0
 > 00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
 > 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
 > 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
 > 0084a000-0084c000 rwxp 0084a000 00:00 0
 > 008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
 > 008bf000-008c rwxp 008bf000 00:00 0
 > 009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
 > 009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
 > 009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
 > 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
 > 00a12000-00a14000 rwxp 00a12000 00:00 0
 > 00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
 > 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
 > 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
 > 00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
 > 00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
 > 00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
 > 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
 > 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
 > 00be2000-00be5000 rwxp 00be2000 00:00 0
 > 00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
 > 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
 > 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
 > 00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
 > 00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
 > 00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
 > 00d3-00d35000 r-xp  fd:00 250619   
/usr/lib/libXdmcp.so.6.0.0
 > 00d35000-00d36000 rwxp 4000 fd:00 250619   
/usr/lib/libXdmcp.so.6.0.0
 > 049e1000-049ec000 r-xp  fd:00 197087
 > /lib/libgcc_s-4.1.2-20080102.so.1
 > 049ec000-049ed000 rwxp a000 fd:00 197087
 > /lib/libgcc_s-4.1.2-20080102.so.1
 > 08048000-082f8000 r-xp  fd:00 1104196   
 > /usr/local/gromacs/bin/mdrun
 > 082f8000-082ff000 rwxp 002b fd:00 1104196   
 > /usr/local/gromacs/bin/mdrun

 > 082ff000-08304000 rwxp 082ff000 00:00 0
 > 09df4000-09e15000 rwxp 09df4000 00:00 0
 > b7e0-b7e21000 rwxp b7e0 00:00 0
 > b7e21000-b7f0 --xp b7e21000 00:00 0
 > bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
 > sh: line 1: 17103 Abortadomdrun > mdrun.out 2>&1
 > FAILED. Check files in rb1
 > 1 out of 16 simple tests FAILED
 > FAILED. Check files in dec+water
 > 1 out of 14 complex tests FAILED
 > All 63 kernel tests PASSED
 > All 45 pdb2gmx tests PASSED
 > I have tried install the gromacs in another machine with Fedora Core 3
 > and the gcc 3.4.4 and i have got similar result
 > ./gmxtest.pl all
 > *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
 > sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
 > FAILED. Check files in rb1
 > 1 out of 16 simple tests FAILED
 > FAILED. Check files in dec+water
 > 1 out of 14 complex tests FAILED
 > All 63 kernel tests PASSED
 > All 45 pdb2gmx tests PASSED
 >
 > So I think that the problem is not because i have used in the firts
 > machine the gcc 4.1.2 compiler. I have seen similar problems in the
 > mailing list, but i didn't find any solutions. Can anybody help me?
 > 
 > Thanks,
 > 
 > Juliana.



Novos endereços, o Yahoo! que você conhece. Crie um email novo 
 
com a sua cara @ymail.com ou @rocketmail.com.

[gmx-users] gmxtest rb1

2008-10-14 Thread Juliana Angeiras 

Hi all,
 
I'm still having problems with the simple test in the directory rb1. I have 
used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the directory 
simple/rb1/ crashed. The complex test dec+water too, but the problem seems not 
too serious as the related in the wiki. The configuration and the output are 
below.
 
Thanks,
 
Juliana.


> I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some 
> problems when i had ran the gmxtest. The output is posted below:
> ./gmxtest.pl all
> *** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***
> === Backtrace: =
> /lib/libc.so.6[0xb0d440]
> /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
> mdrun[0x8136675]
> === Memory map: 
> 00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
> 0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
> 00204000-00205000 rwxp 00204000 00:00 0
> 002bf000-002c rwxp 002bf000 00:00 0
> 004c7000-004c8000 rwxp 004c7000 00:00 0
> 00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
> 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
> 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
> 0084a000-0084c000 rwxp 0084a000 00:00 0
> 008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
> 008bf000-008c rwxp 008bf000 00:00 0
> 009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a12000-00a14000 rwxp 00a12000 00:00 0
> 00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
> 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
> 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
> 00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
> 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
> 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
> 00be2000-00be5000 rwxp 00be2000 00:00 0
> 00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
> 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
> 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
> 00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
> 00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
> 00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
> 00d3-00d35000 r-xp  fd:00 250619    
/usr/lib/libXdmcp.so.6.0.0
> 00d35000-00d36000 rwxp 4000 fd:00 250619    
/usr/lib/libXdmcp.so.6.0.0
> 049e1000-049ec000 r-xp  fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 049ec000-049ed000 rwxp a000 fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 08048000-082f8000 r-xp  fd:00 1104196    
> /usr/local/gromacs/bin/mdrun
> 082f8000-082ff000 rwxp 002b fd:00 1104196    
> /usr/local/gromacs/bin/mdrun
> 082ff000-08304000 rwxp 082ff000 00:00 0
> 09df4000-09e15000 rwxp 09df4000 00:00 0
> b7e0-b7e21000 rwxp b7e0 00:00 0
> b7e21000-b7f0 --xp b7e21000 00:00 0
> bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
> sh: line 1: 17103 Abortado    mdrun > mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> I have tried install the gromacs in another machine with Fedora Core 3 
> and the gcc 3.4.4 and i have got similar result
> ./gmxtest.pl all
> *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
> sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> 
> So I think that the problem is not because i have used in the firts 
> machine the gcc 4.1.2 compiler. I have seen similar problems in the 
> mailing list, but i didn't find any solutions. Can anybody help me?
>  
> Thanks,
>  
> Juliana.



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Re: [gmx-users] gmxtest

2008-10-13 Thread Juliana Angeiras 
Hi,
 
I have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the directory 
simple/rb1/ crashed. The complex test dec+water too, but the problem seems not 
too serious as the related in the wiki.
 
Thanks,
 
Juliana.

--- Em seg, 13/10/08, David van der Spoel <[EMAIL PROTECTED]> escreveu:

De: David van der Spoel <[EMAIL PROTECTED]>
Assunto: Re: [gmx-users] gmxtest
Para: "Discussion list for GROMACS users" 
Data: Segunda-feira, 13 de Outubro de 2008, 16:02

Juliana Angeiras wrote:
> 
> Hi,
>  
> I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some 
> problems when i had ran the gmxtest. The output is posted below:
> ./gmxtest.pl all
> *** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***
> === Backtrace: =
> /lib/libc.so.6[0xb0d440]
> /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
> mdrun[0x8136675]
> === Memory map: 
> 00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
> 0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
> 00204000-00205000 rwxp 00204000 00:00 0
> 002bf000-002c rwxp 002bf000 00:00 0
> 004c7000-004c8000 rwxp 004c7000 00:00 0
> 00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
> 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
> 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
> 0084a000-0084c000 rwxp 0084a000 00:00 0
> 008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
> 008bf000-008c rwxp 008bf000 00:00 0
> 009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a12000-00a14000 rwxp 00a12000 00:00 0
> 00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
> 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
> 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
> 00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
> 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
> 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
> 00be2000-00be5000 rwxp 00be2000 00:00 0
> 00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
> 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
> 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
> 00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
> 00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
> 00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
> 00d3-00d35000 r-xp  fd:00 250619
/usr/lib/libXdmcp.so.6.0.0
> 00d35000-00d36000 rwxp 4000 fd:00 250619
/usr/lib/libXdmcp.so.6.0.0
> 049e1000-049ec000 r-xp  fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 049ec000-049ed000 rwxp a000 fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 08048000-082f8000 r-xp  fd:00 1104196
> /usr/local/gromacs/bin/mdrun
> 082f8000-082ff000 rwxp 002b fd:00 1104196
> /usr/local/gromacs/bin/mdrun
> 082ff000-08304000 rwxp 082ff000 00:00 0
> 09df4000-09e15000 rwxp 09df4000 00:00 0
> b7e0-b7e21000 rwxp b7e0 00:00 0
> b7e21000-b7f0 --xp b7e21000 00:00 0
> bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
> sh: line 1: 17103 Abortadomdrun > mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> I have tried install the gromacs in another machine with Fedora Core 3 
> and the gcc 3.4.4 and i have got similar result
> ./gmxtest.pl all
> *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
> sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> 
> So I think that the problem is not because i have used in the firts 
> machine the gcc 4.1.2 compiler. I have seen similar problems in the 
> mailing list, but i didn't find any solutions. Can anybody help me?
>  
> Thanks,
>  
> Juliana.
Which gromacs version?
Exactly which test crashes, is it rb1?

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Bio

Re: [gmx-users] gmxtest

2008-10-13 Thread Juliana Angeiras 
Hi,
 
I have used gromacs 3.3.3 and gmxtest 3.3.3. The simple test in the directory 
simple/rb1/ crashed. The complex test dec+water too, but the problem seems not 
too serious as the related in the wiki.
 
Thanks,
 
Juliana.

--- Em seg, 13/10/08, David van der Spoel <[EMAIL PROTECTED]> escreveu:

De: David van der Spoel <[EMAIL PROTECTED]>
Assunto: Re: [gmx-users] gmxtest
Para: "Discussion list for GROMACS users" 
Data: Segunda-feira, 13 de Outubro de 2008, 16:02

Juliana Angeiras wrote:
> 
> Hi,
>  
> I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some 
> problems when i had ran the gmxtest. The output is posted below:
> ./gmxtest.pl all
> *** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***
> === Backtrace: =
> /lib/libc.so.6[0xb0d440]
> /lib/libc.so.6(realloc+0x1a7)[0xb0e377]
> mdrun[0x8136675]
> === Memory map: 
> 00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
> 0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
> 00204000-00205000 rwxp 00204000 00:00 0
> 002bf000-002c rwxp 002bf000 00:00 0
> 004c7000-004c8000 rwxp 004c7000 00:00 0
> 00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
> 00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
> 00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
> 0084a000-0084c000 rwxp 0084a000 00:00 0
> 008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
> 008bf000-008c rwxp 008bf000 00:00 0
> 009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
> 009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
> 00a12000-00a14000 rwxp 00a12000 00:00 0
> 00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
> 00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
> 00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
> 00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
> 00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
> 00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
> 00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
> 00be2000-00be5000 rwxp 00be2000 00:00 0
> 00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
> 00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
> 00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
> 00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
> 00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
> 00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
> 00d3-00d35000 r-xp  fd:00 250619
/usr/lib/libXdmcp.so.6.0.0
> 00d35000-00d36000 rwxp 4000 fd:00 250619
/usr/lib/libXdmcp.so.6.0.0
> 049e1000-049ec000 r-xp  fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 049ec000-049ed000 rwxp a000 fd:00 197087 
> /lib/libgcc_s-4.1.2-20080102.so.1
> 08048000-082f8000 r-xp  fd:00 1104196
> /usr/local/gromacs/bin/mdrun
> 082f8000-082ff000 rwxp 002b fd:00 1104196
> /usr/local/gromacs/bin/mdrun
> 082ff000-08304000 rwxp 082ff000 00:00 0
> 09df4000-09e15000 rwxp 09df4000 00:00 0
> b7e0-b7e21000 rwxp b7e0 00:00 0
> b7e21000-b7f0 --xp b7e21000 00:00 0
> bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
> sh: line 1: 17103 Abortadomdrun > mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> I have tried install the gromacs in another machine with Fedora Core 3 
> and the gcc 3.4.4 and i have got similar result
> ./gmxtest.pl all
> *** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
> sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
> FAILED. Check files in rb1
> 1 out of 16 simple tests FAILED
> FAILED. Check files in dec+water
> 1 out of 14 complex tests FAILED
> All 63 kernel tests PASSED
> All 45 pdb2gmx tests PASSED
> 
> So I think that the problem is not because i have used in the firts 
> machine the gcc 4.1.2 compiler. I have seen similar problems in the 
> mailing list, but i didn't find any solutions. Can anybody help me?
>  
> Thanks,
>  
> Juliana.
Which gromacs version?
Exactly which test crashes, is it rb1?

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Bio

Re: [gmx-users] gmxtest

2008-10-13 Thread David van der Spoel 

Juliana Angeiras wrote:


Hi,
 
I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some 
problems when i had ran the gmxtest. The output is posted below:

./gmxtest.pl all
*** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***
=== Backtrace: =
/lib/libc.so.6[0xb0d440]
/lib/libc.so.6(realloc+0x1a7)[0xb0e377]
mdrun[0x8136675]
=== Memory map: 
00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
00204000-00205000 rwxp 00204000 00:00 0
002bf000-002c rwxp 002bf000 00:00 0
004c7000-004c8000 rwxp 004c7000 00:00 0
00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
0084a000-0084c000 rwxp 0084a000 00:00 0
008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
008bf000-008c rwxp 008bf000 00:00 0
009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
00a12000-00a14000 rwxp 00a12000 00:00 0
00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
00be2000-00be5000 rwxp 00be2000 00:00 0
00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
00d3-00d35000 r-xp  fd:00 250619 /usr/lib/libXdmcp.so.6.0.0
00d35000-00d36000 rwxp 4000 fd:00 250619 /usr/lib/libXdmcp.so.6.0.0
049e1000-049ec000 r-xp  fd:00 197087 
/lib/libgcc_s-4.1.2-20080102.so.1
049ec000-049ed000 rwxp a000 fd:00 197087 
/lib/libgcc_s-4.1.2-20080102.so.1
08048000-082f8000 r-xp  fd:00 1104196
/usr/local/gromacs/bin/mdrun
082f8000-082ff000 rwxp 002b fd:00 1104196
/usr/local/gromacs/bin/mdrun

082ff000-08304000 rwxp 082ff000 00:00 0
09df4000-09e15000 rwxp 09df4000 00:00 0
b7e0-b7e21000 rwxp b7e0 00:00 0
b7e21000-b7f0 --xp b7e21000 00:00 0
bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
sh: line 1: 17103 Abortadomdrun > mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
I have tried install the gromacs in another machine with Fedora Core 3 
and the gcc 3.4.4 and i have got similar result

./gmxtest.pl all
*** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED

So I think that the problem is not because i have used in the firts 
machine the gcc 4.1.2 compiler. I have seen similar problems in the 
mailing list, but i didn't find any solutions. Can anybody help me?
 
Thanks,
 
Juliana.

Which gromacs version?
Exactly which test crashes, is it rb1?

--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] gmxtest

2008-10-13 Thread Juliana Angeiras 
Hi,
 
I have installed in my pc centOS 5.2 with gcc 4.1.2 and i had some problems 
when i had ran the gmxtest. The output is posted below:
./gmxtest.pl all
*** glibc detected *** mdrun: realloc(): invalid next size: 0x09e070d0 ***
=== Backtrace: =
/lib/libc.so.6[0xb0d440]
/lib/libc.so.6(realloc+0x1a7)[0xb0e377]
mdrun[0x8136675]
=== Memory map: 
00101000-0020 r-xp  fd:00 250620 /usr/lib/libX11.so.6.2.0
0020-00204000 rwxp 000ff000 fd:00 250620 /usr/lib/libX11.so.6.2.0
00204000-00205000 rwxp 00204000 00:00 0 
002bf000-002c rwxp 002bf000 00:00 0 
004c7000-004c8000 rwxp 004c7000 00:00 0 
00835000-00848000 r-xp  fd:00 197077 /lib/libnsl-2.5.so
00848000-00849000 r-xp 00012000 fd:00 197077 /lib/libnsl-2.5.so
00849000-0084a000 rwxp 00013000 fd:00 197077 /lib/libnsl-2.5.so
0084a000-0084c000 rwxp 0084a000 00:00 0 
008bb000-008bc000 r-xp 008bb000 00:00 0  [vdso]
008bf000-008c rwxp 008bf000 00:00 0 
009e8000-009f r-xp  fd:00 250635 /usr/lib/libSM.so.6.0.0
009f-009f1000 rwxp 7000 fd:00 250635 /usr/lib/libSM.so.6.0.0
009fa000-00a11000 r-xp  fd:00 250634 /usr/lib/libICE.so.6.3.0
00a11000-00a12000 rwxp 00016000 fd:00 250634 /usr/lib/libICE.so.6.3.0
00a12000-00a14000 rwxp 00a12000 00:00 0 
00a7f000-00a99000 r-xp  fd:00 197064 /lib/ld-2.5.so
00a99000-00a9a000 r-xp 00019000 fd:00 197064 /lib/ld-2.5.so
00a9a000-00a9b000 rwxp 0001a000 fd:00 197064 /lib/ld-2.5.so
00a9d000-00a9f000 r-xp  fd:00 250618 /usr/lib/libXau.so.6.0.0
00a9f000-00aa rwxp 1000 fd:00 250618 /usr/lib/libXau.so.6.0.0
00aa2000-00bdf000 r-xp  fd:00 197065 /lib/libc-2.5.so
00bdf000-00be1000 r-xp 0013c000 fd:00 197065 /lib/libc-2.5.so
00be1000-00be2000 rwxp 0013e000 fd:00 197065 /lib/libc-2.5.so
00be2000-00be5000 rwxp 00be2000 00:00 0 
00be7000-00c0c000 r-xp  fd:00 197072 /lib/libm-2.5.so
00c0c000-00c0d000 r-xp 00024000 fd:00 197072 /lib/libm-2.5.so
00c0d000-00c0e000 rwxp 00025000 fd:00 197072 /lib/libm-2.5.so
00c1-00c12000 r-xp  fd:00 197066 /lib/libdl-2.5.so
00c12000-00c13000 r-xp 1000 fd:00 197066 /lib/libdl-2.5.so
00c13000-00c14000 rwxp 2000 fd:00 197066 /lib/libdl-2.5.so
00d3-00d35000 r-xp  fd:00 250619 /usr/lib/libXdmcp.so.6.0.0
00d35000-00d36000 rwxp 4000 fd:00 250619 /usr/lib/libXdmcp.so.6.0.0
049e1000-049ec000 r-xp  fd:00 197087 
/lib/libgcc_s-4.1.2-20080102.so.1
049ec000-049ed000 rwxp a000 fd:00 197087 
/lib/libgcc_s-4.1.2-20080102.so.1
08048000-082f8000 r-xp  fd:00 1104196    /usr/local/gromacs/bin/mdrun
082f8000-082ff000 rwxp 002b fd:00 1104196    /usr/local/gromacs/bin/mdrun
082ff000-08304000 rwxp 082ff000 00:00 0 
09df4000-09e15000 rwxp 09df4000 00:00 0 
b7e0-b7e21000 rwxp b7e0 00:00 0 
b7e21000-b7f0 --xp b7e21000 00:00 0 
bfdbd000-bfdd4000 rwxp bfdbd000 00:00 0  [stack]
sh: line 1: 17103 Abortado    mdrun > mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED
I have tried install the gromacs in another machine with Fedora Core 3 and the 
gcc 3.4.4 and i have got similar result
./gmxtest.pl all
*** glibc detected *** realloc(): invalid next size: 0x08a48f88 ***
sh: line 1: 12569 Aborted mdrun >mdrun.out 2>&1
FAILED. Check files in rb1
1 out of 16 simple tests FAILED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 45 pdb2gmx tests PASSED

So I think that the problem is not because i have used in the firts machine the 
gcc 4.1.2 compiler. I have seen similar problems in the mailing list, but i 
didn't find any solutions. Can anybody help me?
 
Thanks,
 
Juliana.



  Novos endereços, o Yahoo! que você conhece. Crie um email novo com a sua 
cara @ymail.com ou @rocketmail.com.
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[gmx-users] gmxtest, error during pdb2gmx step.

2008-04-28 Thread SeungPyo Hong 
Dear gmx-users,

Recently I installed Gromacs to a new cluster, SUN X4100, Dual Core AMD
Opteron (tm) Processor.
However during the test step, errors occur.
The following is the entire output of the "*$./gmxtest.pl -double all*"
command

All 16 simple tests PASSED
All 14 complex tests PASSED
All 63 kernel tests PASSED
N  Reference   This test
  10-39.0984-32.5043
  11-39.0984-32.5043
  12-93.8123-75.8897
  13-93.8123-75.8897
  21-11007.5-9915.17
There were 5 differences in final energy with the reference file
All 45 pdb2gmx tests PASSED
pdb2gmx tests *FAILED*

I guess this seems to be a comparison between the precalculated
value(Reference) and the value calculated in my machine(This test).

That what is the probable causes of this problem?
I compiled the program again twice,  with *gnu compilers*, gcc.
Also the double precision fftw3 library is used.
Only the installing directory and the fftw3 library directories are given
during configuration.

Additionally, if I use 'xleap' of Amber package and using 'amb2gmx.pl'
script instead of 'pdb2gmx' program, is it OK?
(By doing this I use Amber force field in Gromacs.)
Anyhow, the programs seems to work without out making any troubles, but I
don't know whether I am wasting CPU time or not. ^^

Thank you ~

-- 
--
'God used beautiful mathematics in creating the world.'
-Paul Dirac
'But he created too many objects.'
-Seungpyo Hong

Seungpyo Hong
Master student at PBIL(Protein BioInformatics Lab.) in KAIST, Daejeon Korea
Tel. (82)-18-372-2468
[EMAIL PROTECTED]
[EMAIL PROTECTED]
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[gmx-users] gmxtest failure on a phenom machine

2008-03-26 Thread Giovanni Settanni 
I am testing gromacs 3.3 with lam 7.1.1 on a phenom box with fedora core 8
(old code version of gromacs and lam needed to preserve homogeneity with the
other older opteron boxes in a pc cluster).  gmxtest (for 3.3.2) passes
almost all tests when run on 1 to 3 cores (with -np 1-3 option) (failure on
dec-wat and fe_test occurs always, even on the older boxes of the cluster).
When I try to run the test using all 4 cores ( -np 4 option) a new failure
appears on  simple/rb1. Here is part of the checkpot.out

(...)

comparing energy file reference_s.edr and ener.edr

There are 31 terms in the energy files

There are 4 terms to compare in the energy files

Ryckaert-Bell.   step   1:  0.025919,  step   1:  6.57757
Potentialstep   1:  0.025919,  step   1:  6.57757
Ryckaert-Bell.   step   2: 0.0256805,  step   2:  6.56619
Potentialstep   2: 0.0256805,  step   2:  6.56619
(...)

Any idea about the origin of this error?
Thanks

Gianni
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Re: [gmx-users] gmxtest seems to have missing files

2007-11-29 Thread David van der Spoel 

Amin Astaneh wrote:

Hello gmx-users list:

I downloaded the gmxtest tarball to test my installation. When I ran it, 
I get these errors:

probably meant that you haven't run source GMXRC
test it using the command:
luck



69:0 gmxtest # ./gmxtest.pl simple
No topol.tpr file in angles1. grompp failed
FAILED. Check files in angles1
No topol.tpr file in angles125. grompp failed
FAILED. Check files in angles125
No topol.tpr file in bham. grompp failed
FAILED. Check files in bham
...

It seems that the test suite requires a topol.tpr file in each test case 
directory. There are none.


Thank you for your time.

Amin Astaneh
USF Research Computing
http://rc.usf.edu
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] gmxtest seems to have missing files

2007-11-29 Thread Amin Astaneh 

Hello gmx-users list:

I downloaded the gmxtest tarball to test my installation. When I ran it, 
I get these errors:


69:0 gmxtest # ./gmxtest.pl simple
No topol.tpr file in angles1. grompp failed
FAILED. Check files in angles1
No topol.tpr file in angles125. grompp failed
FAILED. Check files in angles125
No topol.tpr file in bham. grompp failed
FAILED. Check files in bham
...

It seems that the test suite requires a topol.tpr file in each test case 
directory. There are none.


Thank you for your time.

Amin Astaneh
USF Research Computing
http://rc.usf.edu
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[gmx-users] gmxtest results: improper call in complex/acetonitrileRF

2007-10-22 Thread Bruce Ray 
I compiled gromacs 3.3.2 under Mac OS X 10.3.9 with
gcc version 3.3.
I ran the gromacs tests for both single and double
precision and
got the following results:

   %./gmxtest.pl all
   All 16 simple tests PASSED
   FAILED. Check files in acetonitrilRF
   FAILED. Check files in dec+water
   2 out of 14 complex tests FAILED
   All 63 kernel tests PASSED
   All 45 pdb2gmx tests PASSED


   %./gmxtest.pl -double all
   All 16 simple tests PASSED
   FAILED. Check files in acetonitrilRF
   1 out of 14 complex tests FAILED
   All 63 kernel tests PASSED
   All 45 pdb2gmx tests PASSED



In the single precision dec+water test, the error was
from numerical
accuracy as shown:

   %tail /complex/dec+water/checkpot.out
   
   comparing energy file reference_s.edr and ener.edr
   
   There are 41 terms in the energy files
   
   There are 5 terms to compare in the energy files
   
   LJ (SR)  step  34:  -0.21167,  step 
34: -0.17627
   
   Files read succesfully



However, the error in acetonitrilRF is a call that
should not
have been made:

   %tail -30 complex/acetonitrilRF/md.log
   
   Initializing LINear Constraint Solver
 number of constraints is 526
 average number of constraints coupled to one
constraint is 0.0

  Rel. Constraint Deviation:  Maxbetween atoms
RMS
  Before LINCS 0.004201766767 
 0.001573
   After LINCS 0.01454455 
 0.00

   
   Constraining the coordinates at t0-dt (step -1)
  Rel. Constraint Deviation:  Maxbetween atoms
RMS
  Before LINCS 0.000121796797 
 0.45
   After LINCS 0.01685686 
 0.00

   Started mdrun on node 0 Mon Oct 22 08:47:16 2007
   Initial temperature: 326.673 K
   Configuring nonbonded kernels...
   
   
   
  
---
   Program mdrun, VERSION 3.3.2
   Source code file: network.c, line: 437
   
   Routine should not have been called:
   gmx_sumi
  
---
   
   "Is That a Real Poncho ?" (F. Zappa)
   


Sincerely,


-- 
Bruce D. Ray, Ph.D.
Associate Scientist, and Operations Director
NMR Center
IUPUI
Physics Dept.
402 N. Blackford St.
Indianapolis, IN  46202-3273


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