subject:"Re\: \[Freesurfer\] mri_cvs_register error \: PETSC Error"

Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-21 Thread Lilla Zollei



At the moment, unfortunately, not as the high resolution morphs are very 
large.

Lilla

On Mon, 20 Feb 2017, Bhavana Ganesh wrote:


Hi Lilla,
Is there a work around for this because I would at max be able to allocate 8GB 
for the tool but I dont have the resource for 35GB.

Regards,
Bhavana
  [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]


On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei  
wrote:

  Hi Bhavana,

  We recommend to assign about 35GB of RAM on our cluster nodes for this 
operation. I am not sure how that compares to your VB.

  Lilla

  On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

Hi Lilla,
I have allocated 40GB for my VB and 3GB of RAM space. I am not 
allocating anything specific to the function.

Regards,
Bhavana
      [linkedin-logo_318-50643.jpg] 
[world-wide-web-icon-for-website.png]


On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei 
 wrote:

      Hi Bhavana,

      How much memory are you allocating to this process?

      Lilla

      On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

      > Hi Developers,
      >
      > I'm receiving this error while I try to run 
mri_cvs_register. The same error was received when I reran the same even after 
increasing the memory allocated to my VB.
Can anybody help me with the issue I am facing.
      > Below are the details of my system and software 
configurations.
      > PFA error log files.
      >
      > FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
      > Platform: CentOS7 on VirtualBox
      >
      > Command Run:
      >
      > mri_cvs_register --mov bert2
      >
      >
      > 0]PETSC ERROR: - Error Message 

      >
      > [0]PETSC ERROR: Out of memory. This could be due to 
allocating
      > [0]PETSC ERROR: too large an object or bleeding by not 
properly
      > [0]PETSC ERROR: destroying unneeded objects.
      > [0]PETSC ERROR: Memory allocated 0 Memory used by process 
-2147483648
      > [0]PETSC ERROR: Try running with -malloc_dump or 
-malloc_log for info.
      > [0]PETSC ERROR: Memory requested 576224344!
      > [0]PETSC ERROR: 

      > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu 
May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
      > [0]PETSC ERROR: See docs/changes/index.html for recent 
updates.
      > [0]PETSC ERROR: See docs/faq.html for hints about trouble 
shooting.
      > [0]PETSC ERROR: See docs/index.html for manual pages.
      > [0]PETSC ERROR: 

      > [0]PETSC ERROR: surf2vol on a linux-gnu named 
localhost.localdomain by root Thu Feb 16 09:57:44 2017
      > [0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
      > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
      > [0]PETSC ERROR: Configure options --with-debugging=no 
--with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 
--with-mpi=1 --with-x=0
--with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
      > [0]PETSC ERROR: 

      > [0]PETSC ERROR: PetscMallocAlign() line 61 in 
src/sys/memory/mal.c
      > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 
2818 in src/mat/impls/aij/seq/aij.c
      > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in 
src/mat/impls/aij/seq/aij.c
      > [0]PETSC ERROR: MatTranspose() line 3500 in 
src/mat/interface/matrix.c
      > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in 
unknowndirectory/solver.h
      >  after setup_load_mfc
      > Linear solve converged due to CONVERGED_ITS iterations 1
      >
      > Thank You
      >
      > Regards,
      > Bhavana
>       [linkedin-logo_318-50643.jpg] 
[world-wide-web-icon-for-website.png]
>
>
>
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-20 Thread Bhavana Ganesh

Hi Lilla,
Is there a work around for this because I would at max be able to allocate
8GB for the tool but I dont have the resource for 35GB.

*Regards,*
*Bhavana*







On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei 
wrote:

>
> Hi Bhavana,
>
> We recommend to assign about 35GB of RAM on our cluster nodes for this
> operation. I am not sure how that compares to your VB.
>
> Lilla
>
> On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>
> Hi Lilla,
>> I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating
>> anything specific to the function.
>>
>> Regards,
>> Bhavana
>>   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
>>
>>
>>
>> On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei <
>> lzol...@nmr.mgh.harvard.edu> wrote:
>>
>>   Hi Bhavana,
>>
>>   How much memory are you allocating to this process?
>>
>>   Lilla
>>
>>   On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>>
>>   > Hi Developers,
>>   >
>>   > I'm receiving this error while I try to run mri_cvs_register. The
>> same error was received when I reran the same even after increasing the
>> memory allocated to my VB. Can anybody help me with the issue I am facing.
>>   > Below are the details of my system and software configurations.
>>   > PFA error log files.
>>   >
>>   > FreeSurfer version: freesurfer-Linux-centos6_x86_6
>> 4-stable-pub-v6.0.0-2beb96c
>>   > Platform: CentOS7 on VirtualBox
>>   >
>>   > Command Run:
>>   >
>>   > mri_cvs_register --mov bert2
>>   >
>>   >
>>   > 0]PETSC ERROR: - Error Message
>> 
>>   >
>>   > [0]PETSC ERROR: Out of memory. This could be due to allocating
>>   > [0]PETSC ERROR: too large an object or bleeding by not properly
>>   > [0]PETSC ERROR: destroying unneeded objects.
>>   > [0]PETSC ERROR: Memory allocated 0 Memory used by process -
>> 2147483648
>>   > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for
>> info.
>>   > [0]PETSC ERROR: Memory requested 576224344!
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
>> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
>>   > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>   > [0]PETSC ERROR: See docs/faq.html for hints about trouble
>> shooting.
>>   > [0]PETSC ERROR: See docs/index.html for manual pages.
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: surf2vol on a linux-gnu named
>> localhost.localdomain by root Thu Feb 16 09:57:44 2017
>>   > [0]PETSC ERROR: Libraries linked from
>> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/pets
>> c/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
>>   > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
>>   > [0]PETSC ERROR: Configure options --with-debugging=no
>> --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1
>> --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0
>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>   > [0]PETSC ERROR: --
>> --
>>   > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
>>   > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in
>> src/mat/impls/aij/seq/aij.c
>>   > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in
>> src/mat/impls/aij/seq/aij.c
>>   > [0]PETSC ERROR: MatTranspose() line 3500 in
>> src/mat/interface/matrix.c
>>   > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in
>> unknowndirectory/solver.h
>>   >  after setup_load_mfc
>>   > Linear solve converged due to CONVERGED_ITS iterations 1
>>   >
>>   > Thank You
>>   >
>>   > Regards,
>>   > Bhavana
>> >   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-websi
>> te.png]
>> >
>> >
>> >
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nm
>> r.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIBAg=clK
>> 7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=nABehjuKoAjknWvzx
>> _wVQA=ZVNYp7GOvkOej8wDnqTeBO0aUk9lYst_itqDG5HCtgo=
>> NFcK8Zziyesd-5JlzLnhEkAycTFrE3zdMqcNdQnXHUM=
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>>

Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-20 Thread Lilla Zollei



Hi Bhavana,

We recommend to assign about 35GB of RAM on our cluster nodes for this 
operation. I am not sure how that compares to your VB.


Lilla

On Mon, 20 Feb 2017, Bhavana Ganesh wrote:


Hi Lilla,
I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating 
anything specific to the function.

Regards,
Bhavana
  [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]


On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei  
wrote:

  Hi Bhavana,

  How much memory are you allocating to this process?

  Lilla

  On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

  > Hi Developers,
  >
  > I'm receiving this error while I try to run mri_cvs_register. The same 
error was received when I reran the same even after increasing the memory 
allocated to my VB. Can anybody help me with the issue I am facing.
  > Below are the details of my system and software configurations.
  > PFA error log files.
  >
  > FreeSurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
  > Platform: CentOS7 on VirtualBox
  >
  > Command Run:
  >
  > mri_cvs_register --mov bert2
  >
  >
  > 0]PETSC ERROR: - Error Message 

  >
  > [0]PETSC ERROR: Out of memory. This could be due to allocating
  > [0]PETSC ERROR: too large an object or bleeding by not properly
  > [0]PETSC ERROR: destroying unneeded objects.
  > [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
  > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
  > [0]PETSC ERROR: Memory requested 576224344!
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 
17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
  > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
  > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
  > [0]PETSC ERROR: See docs/index.html for manual pages.
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by 
root Thu Feb 16 09:57:44 2017
  > [0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
  > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
  > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
  > [0]PETSC ERROR: 

  > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
  > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
src/mat/impls/aij/seq/aij.c
  > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in 
src/mat/impls/aij/seq/aij.c
  > [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
  > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in 
unknowndirectory/solver.h
  >  after setup_load_mfc
  > Linear solve converged due to CONVERGED_ITS iterations 1
  >
  > Thank You
  >
  > Regards,
  > Bhavana
>       [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
>
>
>
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-20 Thread Bhavana Ganesh

Hi Lilla,
I have allocated 40GB for my VB and 3GB of RAM space. I am not allocating
anything specific to the function.

*Regards,*
*Bhavana*







On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei 
wrote:

>
> Hi Bhavana,
>
> How much memory are you allocating to this process?
>
> Lilla
>
> On Mon, 20 Feb 2017, Bhavana Ganesh wrote:
>
> > Hi Developers,
> >
> > I'm receiving this error while I try to run mri_cvs_register. The same
> error was received when I reran the same even after increasing the memory
> allocated to my VB. Can anybody help me with the issue I am facing.
> > Below are the details of my system and software configurations.
> > PFA error log files.
> >
> > FreeSurfer version: freesurfer-Linux-centos6_x86_
> 64-stable-pub-v6.0.0-2beb96c
> > Platform: CentOS7 on VirtualBox
> >
> > Command Run:
> >
> > mri_cvs_register --mov bert2
> >
> >
> > 0]PETSC ERROR: - Error Message
> 
> >
> > [0]PETSC ERROR: Out of memory. This could be due to allocating
> > [0]PETSC ERROR: too large an object or bleeding by not properly
> > [0]PETSC ERROR: destroying unneeded objects.
> > [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
> > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> > [0]PETSC ERROR: Memory requested 576224344!
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15
> 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by
> root Thu Feb 16 09:57:44 2017
> > [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/
> Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.
> 3-p13/lib/linux-gnu-c-opt
> > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> > [0]PETSC ERROR: --
> --
> > [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
> > [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in
> src/mat/impls/aij/seq/aij.c
> > [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in
> src/mat/impls/aij/seq/aij.c
> > [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
> > [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in
> unknowndirectory/solver.h
> >  after setup_load_mfc
> > Linear solve converged due to CONVERGED_ITS iterations 1
> >
> > Thank You
> >
> > Regards,
> > Bhavana
> >   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-
> website.png]
> >
> >
> >
> ___
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> 5JlzLnhEkAycTFrE3zdMqcNdQnXHUM=
>
>
> The information in this e-mail is intended only for the person to whom it
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

2017-02-20 Thread Lilla Zollei


Hi Bhavana,

How much memory are you allocating to this process?

Lilla

On Mon, 20 Feb 2017, Bhavana Ganesh wrote:

> Hi Developers,
> 
> I'm receiving this error while I try to run mri_cvs_register. The same error 
> was received when I reran the same even after increasing the memory allocated 
> to my VB. Can anybody help me with the issue I am facing.
> Below are the details of my system and software configurations.
> PFA error log files.
> 
> FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> Platform: CentOS7 on VirtualBox
> 
> Command Run:
> 
> mri_cvs_register --mov bert2
> 
> 
> 0]PETSC ERROR: - Error Message 
> 
> 
> [0]PETSC ERROR: Out of memory. This could be due to allocating
> [0]PETSC ERROR: too large an object or bleeding by not properly
> [0]PETSC ERROR: destroying unneeded objects.
> [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648
> [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info.
> [0]PETSC ERROR: Memory requested 576224344!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: surf2vol on a linux-gnu named localhost.localdomain by root 
> Thu Feb 16 09:57:44 2017
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c
> [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in 
> src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: MatTranspose_SeqAIJ() line 1460 in src/mat/impls/aij/seq/aij.c
> [0]PETSC ERROR: MatTranspose() line 3500 in src/mat/interface/matrix.c
> [0]PETSC ERROR: TSolver::setup_load_sym() line 1130 in 
> unknowndirectory/solver.h
>  after setup_load_mfc
> Linear solve converged due to CONVERGED_ITS iterations 1
> 
> Thank You
> 
> Regards,
> Bhavana
>   [linkedin-logo_318-50643.jpg] [world-wide-web-icon-for-website.png]
> 
> 
>
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Re: [Freesurfer] mri_cvs_register error : PETSC Error

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Re: [Freesurfer] mri_cvs_register error : PETSC Error

Re: [Freesurfer] mri_cvs_register error : PETSC Error

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