Hi,
I have been trying to build the freesurfer dev version with GPU support as per the information I had from my previous try a couple of months ago that Richard help me to successfully complete and I have not been successful in that.
I followed the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
with slight changes,
After running, cd ~/freesurfer ./setup_configure
I edited the configure file that it generated and then commented out, # with_cuda="" and I changed from CUDA_LIBS="-L$CUDA_DIR/lib $LIB_CUDA -lcudart" to CUDA_LIBS="-L$CUDA_DIR/lib64 $LIB_CUDA -lcudart"
then I executed, ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install --disable-xawplus-apps --disable-tcltk-apps --enable-fermi-gpu --with-cuda="/usr/local/cuda"
Subsequently when I ran make -j4 it worked without any errors. But after that when I run make check I get errors and it fails.
I had sent a previous email regarding the same in another thread but it looks like it has not shown up. So I'm re-sending this now. Infact I have recloned the freesurfer dev version to try it once again and all I get is new errors. Following are the errors now,
Testsuite summary for Freesurfer dev ============================================================================ # TOTAL: 1 # PASS: 0 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0 # ERROR: 0 ============================================================================ See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log Please report to freesurfer@nmr.mgh.harvard.edu ============================================================================ make[5]: *** [test-suite.log] Error 1 make[5]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[4]: *** [check-TESTS] Error 2 make[4]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[3]: *** [check-am] Error 2 make[3]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[2]: *** [check-recursive] Error 1 make[2]: Leaving directory `/media/data1/tyson/freesurfer/utils/test' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/media/data1/tyson/freesurfer/utils' make: *** [check-recursive] Error 1
If you want the log files, let me know and I'll send it as well.
The idea behind trying to build this was see how freesurfer v6 dev version works with GPU. Also would it be possible to use the GPU binaries of mri_em_register and the other register binary and combine it with the current opnmp implemenation in freesurfer v6?
My objective all along has been to reduce it from the current best performance of 4hrs and 38mins to something even lower like 2hrs or lesser on a per subject basis since the subjects are pushed to the server dynamically.
Thanks, Tyson
On 28 February 2017 at 01:10, Francis Tyson Thomas francistthomas@email.arizona.edu wrote:
============================================================================ See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log Please report to freesurfer@nmr.mgh.harvard.edu ============================================================================
That's odd - to my knowledge, that's not a GPU accelerated program.
What does the log say exactly? And which GPU accelerated versions have been run up to this point?
Regards,
Richard
Hi Richard,
I have attached the log file as you had requested.
Thanks,
On Tue, Feb 28, 2017 at 3:36 AM, R Edgar freesurfer.rge@gmail.com wrote:
On 28 February 2017 at 01:10, Francis Tyson Thomas francistthomas@email.arizona.edu wrote:
============================================================
================
See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log Please report to freesurfer@nmr.mgh.harvard.edu ============================================================
================
That's odd - to my knowledge, that's not a GPU accelerated program.
What does the log say exactly? And which GPU accelerated versions have been run up to this point?
Regards,
Richard _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Z K,
I went ahead and tried your suggestion of running *make install *and these are errors I have,
mv ../../distribution/average/?h.EC_average \ /home/tyson/tyson/fs_install/subjects chmod -R 775 /home/tyson/tyson/fs_install/subjects/?h.EC_average rm -Rf /home/tyson/tyson/fs_install/average/mult-comp-cor rm -Rf ../../distribution/average/mult-comp-cor gunzip -c ../../distribution/average/mult-comp-cor.tar.gz | tar xvf - gzip: ../../distribution/average/mult-comp-cor.tar.gz: No such file or directory tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors make[2]: *** [install] Error 2 make[2]: Leaving directory `/media/data1/tyson/freesurfer/distribution/average' make[1]: *** [install-recursive] Error 1 make[1]: Leaving directory `/media/data1/tyson/freesurfer/distribution' make: *** [install-recursive] Error 1
Thanks, Tyson
On Wed, Mar 1, 2017 at 1:28 AM, Francis Tyson Thomas < francistthomas@email.arizona.edu> wrote:
Hi Richard,
I have attached the log file as you had requested.
Thanks,
On Tue, Feb 28, 2017 at 3:36 AM, R Edgar freesurfer.rge@gmail.com wrote:
On 28 February 2017 at 01:10, Francis Tyson Thomas francistthomas@email.arizona.edu wrote:
============================================================
================
See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log Please report to freesurfer@nmr.mgh.harvard.edu ============================================================
================
That's odd - to my knowledge, that's not a GPU accelerated program.
What does the log say exactly? And which GPU accelerated versions have been run up to this point?
Regards,
Richard _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
On 1 March 2017 at 03:28, Francis Tyson Thomas francistthomas@email.arizona.edu wrote:
I have attached the log file as you had requested.
This is the error: gzip: testdata.tar.gz: No such file or directory tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors testdata: No such file or directory.
I believe that git annex is supposed to supply the tarball... Zeke?
Richard
Hello Francis,
Yes, Richard is correct. When doing a local installation you will need the freesurfer data files which do not come with a default clone of the repo. Please see section 1.1 of the build page:
$> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
To get the data files required for installation, you need to type:
$> $> git annex get --metadata fstags=makeinstall .
If you already did that and didnt get the file, its possibly missing the tag (Ill have to double check). If that's the case, just get in manually:
$> git annex get distribution/average/mult-comp-cor.tar.gz $> make install
-Zeke
## Get only the data files required for local installation (4.3 GB) $> git annex get --metadata fstags=makeinstall .
On 1 March 2017 at 03:28, Francis Tyson Thomas francistthomas@email.arizona.edu wrote:
I have attached the log file as you had requested.
This is the error: gzip: testdata.tar.gz: No such file or directory tar: This does not look like a tar archive tar: Exiting with failure status due to previous errors testdata: No such file or directory.
I believe that git annex is supposed to supply the tarball... Zeke?
Richard _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
We are building up our testing infrastructure and as it currently stands it may still be a little too catered to our specific build environment. If freesurfer builds for you than I would skip the 'make check' stage. The best sanity check would be to make a copy of the bert subject folder, re-recon that subject, and compare that with the original bert shipped with freesurfer
On 02/28/2017 01:10 AM, Francis Tyson Thomas wrote:
Hi,
I have been trying to build the freesurfer dev version with GPU support as per the information I had from my previous try a couple of months ago that Richard help me to successfully complete and I have not been successful in that.
I followed the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
with slight changes,
After running, cd ~/freesurfer ./setup_configure
I edited the configure file that it generated and then commented out, # with_cuda="" and I changed from CUDA_LIBS="-L$CUDA_DIR/lib $LIB_CUDA -lcudart" to CUDA_LIBS="-L$CUDA_DIR/lib64 $LIB_CUDA -lcudart"
then I executed, ./configure --disable-Werror --with-pkgs-dir=/home/username/centos6-x86_64-packages --prefix=/home/username/fs_install --disable-xawplus-apps --disable-tcltk-apps --enable-fermi-gpu --with-cuda="/usr/local/cuda"
Subsequently when I ran make -j4 it worked without any errors. But after that when I run make check I get errors and it fails.
I had sent a previous email regarding the same in another thread but it looks like it has not shown up. So I'm re-sending this now. Infact I have recloned the freesurfer dev version to try it once again and all I get is new errors. Following are the errors now,
Testsuite summary for Freesurfer dev
# TOTAL: 1 # PASS: 0 # SKIP: 0 # XFAIL: 0 # FAIL: 1 # XPASS: 0
# ERROR: 0
See utils/test/mriBuildVoronoiDiagramFloat/test-suite.log Please report to freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
make[5]: *** [test-suite.log] Error 1 make[5]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[4]: *** [check-TESTS] Error 2 make[4]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[3]: *** [check-am] Error 2 make[3]: Leaving directory `/media/data1/tyson/freesurfer/utils/test/mriBuildVoronoiDiagramFloat' make[2]: *** [check-recursive] Error 1 make[2]: Leaving directory `/media/data1/tyson/freesurfer/utils/test' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/media/data1/tyson/freesurfer/utils' make: *** [check-recursive] Error 1
If you want the log files, let me know and I'll send it as well.
The idea behind trying to build this was see how freesurfer v6 dev version works with GPU. Also would it be possible to use the GPU binaries of mri_em_register and the other register binary and combine it with the current opnmp implemenation in freesurfer v6?
My objective all along has been to reduce it from the current best performance of 4hrs and 38mins to something even lower like 2hrs or lesser on a per subject basis since the subjects are pushed to the server dynamically.
Thanks, Tyson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Francis Tyson Thomas -
R Edgar -
Z K -
zkaufman＠nmr.mgh.harvard.edu