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 <%28214%29%20748-3648> [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*
https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh http://bhavanaganesh.weebly.com/
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]
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*
https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh http://bhavanaganesh.weebly.com/
On Mon, Feb 20, 2017 at 12:21 PM, Lilla Zollei lzollei@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_
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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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 lzollei@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_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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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*
https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh https://www.linkedin.com/in/bhavanaganesh http://bhavanaganesh.weebly.com/
On Mon, Feb 20, 2017 at 4:43 PM, Lilla Zollei lzollei@nmr.mgh.harvard.edu 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 < lzollei@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. Thesame 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 1517:29:26 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 namedlocalhost.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 insrc/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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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 lzollei@nmr.mgh.harvard.edu 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 <lzollei@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_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] > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... kOej8wDnqTeBO0aUk9lYst_itqDG5HCtgo&s=NFcK8Zziyesd-5JlzLnhEkAycTFrE3zdMqcNdQnXHUM&e=
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Lilla Zollei