Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30132 discussions

Re: [Freesurfer] CUDA error
by orangekic 25 Aug '10

25 Aug '10

Hello, I am running FS V5.0 on personal computer outside the Martinos Center. The OS is CentOS 5.5, and the hardware is NVIDIA Geforce 8500 GT graphic card with latest driver (NVIDIA-Linux-x86_64-256.44.run). CPU: Intel(R) Core(TM)2 CPU 4400 @ 2.00GHz Thanks for your help. p.s. I made some mistake in the previous mail, which the CUDA toolkit 3.1 is for RedHat Enterprise 5.3. 2010/8/25 Help Desk Elf --- Chris Johnson <help(a)nmr.mgh.harvard.edu> What computer are you running this on? If you are doing this > from within the Martinos Center, we are having hardware problems with > the storage cluster on which freesurfer resides. > > > Hi, >> >> I have Install CUDA toolkit 3.1 (for Ubuntu Linux 9.10), >> 'fscudabins-linux-centos4_x86_64.tgz', and update the NVIDIA driver. >> And compiled as "recon-all -all -s subject1 -use-gpu" >> >> However, I got the CUDA error message: >> "CUDA error in file >> '/space/freesurfer/build/minerva/stable/dev/include/volmegpu_imp1.hpp' on >> line 104 : invalid argument." >> >> how can I solve this problem? >> >> Best, >> >> Kung. >> >> >> > > ------------------------------------------------------------------------------- > Chris Johnson |Internet: johnson(a)nmr.mgh.harvard.edu > Systems Administrator |Web: > http://www.nmr.mgh.harvard.edu/~johnson > NMR Center |Voice: 617.726.0949 > Mass. General Hospital |FAX: 617.726.7422 > 149 (2301) 13th Street |A lifetime is more than sufficiently long > Charlestown, MA., 02129 USA |to get what there is of it wrong. Piet Hein > > ------------------------------------------------------------------------------- > > > 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. > >

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CUDA error
by orangekic 25 Aug '10

25 Aug '10

Hi, I have Install CUDA toolkit 3.1 (for Ubuntu Linux 9.10), 'fscudabins-linux-centos4_x86_64.tgz', and update the NVIDIA driver. And compiled as "recon-all -all -s subject1 -use-gpu" However, I got the CUDA error message: "CUDA error in file '/space/freesurfer/build/minerva/stable/dev/include/volmegpu_imp1.hpp' on line 104 : invalid argument." how can I solve this problem? Best. -- Yi-Chia Kung 龔怡嘉 Brain Connectivity Laboratory Institute of Biomedical Imaging and Radiological Sciences National Yang-Ming University Taipei, Taiwan Tel: +886 2 28267000 #6134

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how to expand the disk size if I use VirtualBoxFS45
by Guang Zeng 24 Aug '10

24 Aug '10

Hi, there, I am using VirtualBoxFS45 now, everything is fine. But I find that after I load the FSVirtualBox.vdi, the default storage space is about 8GB. I'd like to use FreeSurfer to run multiple subjects (about 100), and then do group analysis using QDEC, however the 8GB disk space limit will be a big problem. Anyone know how to expand (or change) the default 8GB disk space in VirtualBox? Thanks a lot! Guang

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CUDA error...
by Gonzalo Rojas Costa 24 Aug '10

24 Aug '10

Hi: I installed the latest NVIDIA driver (256.44) in my DELL Precision T3500 (Quadro FX-580 graphic board, Ubuntu 9.04)... Then I installed CUDA Toolit 3.1 (for Ubuntu 9.10)... Then, I restart my computer... I tried to process a study with the freesurfer command: "recon-all -autorecon1 -s ingrid -use-gpu", but I got the error: "/home/gonzalorojas/freesurfer/subjects/ingrid/mri mri_em_register_cuda -skull nu.mgz /home/gonzalorojas/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta Acquiring CUDA device Using default device CUDA Error in file 'devicemanagement.cu' on line 46 : unspecified driver error. Linux image 2.6.28-17-generic #58-Ubuntu SMP Tue Dec 1 18:57:07 UTC 2009 i686 GNU/Linux recon-all -s ingrid exited with ERRORS at Tue Aug 24 11:46:20 CLT 2010" How can I find a solution to that problem ?... Sincerely, Gonzalo Rojas Costa

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From mgz to m3z
by Soon Hock Wei 24 Aug '10

24 Aug '10

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Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 42
by Gonzalo Rojas Costa 24 Aug '10

24 Aug '10

Hi: Any solution for the 32 bit version ?... Sincerely, Gonzalo Rojas Costa > Message: 6 > Date: Fri, 20 Aug 2010 15:55:39 -0400 > From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] CUDA Error - all CUDA-capable devices are > busy or unavailable > To: Daniel Guellmar <Daniel.Guellmar(a)med.uni-jena.de> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <1282334139.31414.17.camel(a)terrier.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8 > > CUDA users, > > The problem with the _cuda binaries (message: CUDA Error in file > 'devicemanagement.cu'...) has been fixed, and new binaries are available > for download from here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… > > download the file 'fscudabins-linux-centos4_x86_64.tgz' and extract it > (tar zxvf <filename>) into your $FREESURFER_HOME/bin directory. This is > for the 64b linux platform only (centos 4 and 5). > > fyi, the problem was that the utility UPX, which is run on the publicly > distributed freesurfer binaries to reduce their size, seemed to cause > this strange problem. > > Let us know how these utilities work. In particular we'd like to get a > sense of the type of NVIDIA GPU cards people are using. > > Nick >

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Antw: Re: Antw: Re: CUDA Error - all CUDA-capable devices are busy or unavailable
by Daniel Guellmar 23 Aug '10

23 Aug '10

ls -alF `which mri_em_register_cuda` says -rwxrwxr-x 1 6635 160 28831410 2010-08-18 13:56 /opt/medphys/freesurfer/5.0.0-amd64/bin/mri_em_register_cuda* Adding a time shift of 6 hours (germany) the create time is 07:56 ... ldd of the binary shows ldd /opt/medphys/freesurfer/5.0.0-amd64/bin/mri_em_register_cuda linux-vdso.so.1 => (0x00007fff2b5a2000) libcuda.so.1 => /usr/lib/libcuda.so.1 (0x00007f6781e9b000) libcudart.so.3 => /opt/medphys/cuda/cuda-toolkit-current/lib64/libcudart.so.3 (0x00007f6781c68000) libz.so.1 => /lib/libz.so.1 (0x00007f6781a51000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00007f6781818000) libdl.so.2 => /lib/libdl.so.2 (0x00007f6781614000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007f67813f8000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f67810e8000) libm.so.6 => /lib/libm.so.6 (0x00007f6780e64000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f6780c4d000) libc.so.6 => /lib/libc.so.6 (0x00007f67808dd000) librt.so.1 => /lib/librt.so.1 (0x00007f67806d5000) /lib64/ld-linux-x86-64.so.2 (0x00007f6782883000) the libcuda.so.1 links to /usr/lib/libcuda.so.256.40 ... which version do you use at the center? Daniel >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 23.08.10 20.23 Uhr >>> is the date on your mri_em_register_cuda 'Aug 18 07:56'? to see this, type: ls -alF `which mri_em_register_cuda` i've just re-downloaded the fscudabins-linux-centos4_x86_64.tgz tarball and tested mri_em_register_cuda on a C1060 we have and it seems to work. n. On Mon, 2010-08-23 at 12:42 +0200, Daniel Guellmar wrote: > Hi Nick, > > thank you for your quick reply and the explanation. Unfortunately the > new binary still do not work. The error message changes now to .. > > Acquiring CUDA device > Using default device > CUDA Error in file 'devicemanagement.cu' on line 46 : invalid > argument. > > This error occurs on a Tesla C1060 and on Tesla C2050. I haven't tried > on regular GPU cards, but will manage to do so in the next days ... > > Any ideas, what could be wrong? > > Daniel > > >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> schrieb am 8/20/2010 um > 9:55 in > Nachricht <1282334139.31414.17.camel(a)terrier.nmr.mgh.harvard.edu>: > > CUDA users, > > > > The problem with the _cuda binaries (message: CUDA Error in file > > 'devicemanagement.cu'...) has been fixed, and new binaries are > available > > for download from here: > > > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86_ > > > 64/ > > > > download the file 'fscudabins-linux-centos4_x86_64.tgz' and extract > it > > (tar zxvf <filename>) into your $FREESURFER_HOME/bin directory. This > is > > for the 64b linux platform only (centos 4 and 5). > > > > fyi, the problem was that the utility UPX, which is run on the > publicly > > distributed freesurfer binaries to reduce their size, seemed to > cause > > this strange problem. > > > > Let us know how these utilities work. In particular we'd like to get > a > > sense of the type of NVIDIA GPU cards people are using. > > > > Nick > > > > > > On Thu, 2010-08-19 at 12:57 -0400, Nick Schmansky wrote: > >> hello cuda beta users! this problem 'all CUDA-capable > >> devices are busy or unavailable.', seems to fall into the category > of > >> 'post-release curse', because i am seeing this problem locally as > well, > >> but havent seen it in the months we've been using the gpu code. we > have > >> found rebooting the machine seems to work, but thats not a real > >> solution. i suspect our detection scheme is tripping a flag in the > >> driver thats not getting untripped or cleared the next time around. > >> > >> when we find a better solution, we'll post new _cuda libs on our > site, > >> which i'm expecting will be a regular occurrence over the next few > >> months. glad to see so many willing gpu users though! > >> > >> n. > >> > >> > >> On Thu, 2010-08-19 at 17:08 +0200, Daniel Guellmar wrote: > >> > Hi folks, > >>> >> > I'm trying to employ the new cuda binaries, which come with > freesurfer > >> > version 5.0.0, however, if I'm trying to execute a cuda binary > (e.g. > >> > mri_ca_register_cuda) I get the following output: > >> > > >> > Acquiring CUDA device > >> > Using default device > >> > CUDA Error in file 'devicemanagement.cu' on line 46 : all > CUDA-capable > >> > devices are busy or unavailable. > >> > > >> > This error occurs on two different systems which are cuda capable. > Both > >> > systems run with Ubuntu 9.10, both have the latest developer > driver for > >> > linux (256.40) and the latest cuda toolkit (3.1) on it. The GPU > >> > Computing SDK code samples compile and work fine. The device query > on > >> > both hosts work fine ... see following output > >> > > >> > Host 1: > >> > > >> > CUDA Device Query (Runtime API) version (CUDART static linking) > >> > > >> > There are 2 devices supporting CUDA > >> > > >> > Device 0: "Tesla C2050" > >> > CUDA Driver Version: 3.10 > >> > CUDA Runtime Version: 3.10 > >> > CUDA Capability Major revision number: 2 > >> > CUDA Capability Minor revision number: 0 > >> > Total amount of global memory: 2817720320 bytes > >> > Number of multiprocessors: 14 > >> > Number of cores: 448 > >> > Total amount of constant memory: 65536 bytes > >> > Total amount of shared memory per block: 49152 bytes > >> > Total number of registers available per block: 32768 > >> > Warp size: 32 > >> > Maximum number of threads per block: 1024 > >> > Maximum sizes of each dimension of a block: 1024 x 1024 x 64 > >> > Maximum sizes of each dimension of a grid: 65535 x 65535 x > 1 > >> > Maximum memory pitch: 2147483647 bytes > >> > Texture alignment: 512 bytes > >> > Clock rate: 1.15 GHz > >> > Concurrent copy and execution: Yes > >> > Run time limit on kernels: Yes > >> > Integrated: No > >> > Support host page-locked memory mapping: Yes > >> > Compute mode: Default (multiple > host > >> > threads can use this device simultaneously) > >> > Concurrent kernel execution: Yes > >> > Device has ECC support enabled: Yes > >> > > >> > Device 1: "Tesla C2050" > >> > CUDA Driver Version: 3.10 > >> > CUDA Runtime Version: 3.10 > >> > CUDA Capability Major revision number: 2 > >> > CUDA Capability Minor revision number: 0 > >> > Total amount of global memory: 2817982464 bytes > >> > Number of multiprocessors: 14 > >> > Number of cores: 448 > >> > Total amount of constant memory: 65536 bytes > >> > Total amount of shared memory per block: 49152 bytes > >> > Total number of registers available per block: 32768 > >> > Warp size: 32 > >> > Maximum number of threads per block: 1024 > >> > Maximum sizes of each dimension of a block: 1024 x 1024 x 64 > >> > Maximum sizes of each dimension of a grid: 65535 x 65535 x > 1 > >> > Maximum memory pitch: 2147483647 bytes > >> > Texture alignment: 512 bytes > >> > Clock rate: 1.15 GHz > >> > Concurrent copy and execution: Yes > >> > Run time limit on kernels: Yes > >> > Integrated: No > >> > Support host page-locked memory mapping: Yes > >> > Compute mode: > >> > threads can use this device simultaneously) > >> > Concurrent kernel execution: Yes > >> > Device has ECC support enabled: Yes > >> > > >> > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 3.10, > CUDA > >> > Runtime Version = 3.10, NumDevs = 2, Device = Tesla C2050, Device > = > >> > Tesla C2050 > >> > > >> > > >> > Host 2: > >> > > >> > CUDA Device Query (Runtime API) version (CUDART static linking) > >> > > >> > There is 1 device supporting CUDA > >> > > >> > Device 0: "Tesla C1060" > >> > CUDA Driv CUDA Runtime Version: 3.10 > >> > CUDA Capability Major revision number: 1 > >> > CUDA Capability Minor revision number: 3 > >> > Total amount of global memory: 4294770688 bytes > >> > Number of multiprocessors: 30 > >> > Number of cores: 240 > >> > Total amount of constant memory: 65536 bytes > >> > Total amount of shared memory per block: 16384 bytes > >> > Total number of registers available per block: 16384 > >> > Warp size: 32 > >> > Maximum number of threads per block: 512 > >> > Maximum sizes of each dimension of a block: 512 x 512 x 64 > >> > Maximum sizes of each dimension of a grid: 65535 x 65535 x > 1 > >> > Maximum memory pitch: 2147483647 bytes > >> > Texture alignment: 256 bytes > >> > Clock rate: 1.30 GHz > >> > Concurrent copy and execution: Yes > >> > Run time limit on kernels: No > >> > Integrated: No > >> > Support host page-locked memory mapping: Yes > >> > Compute mode: Default (multiple > host > >> > threads can use this device simultaneously) > >> > Concurrent kernel execution: No > >> > Device has ECC support enabled: No > >> > > >> > deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 3.10, > CUDA > >> > Runtime Version = 3.10, NumDevs = 1, Device = Tesla C1060 > >> > > >> > Any comments on that? > >> > > >> > Regards and thanks in advance, > >> > Daniel > >> > > >> > > >> > -- > >> > > >> > Dr.-Ing. Daniel Güllmar > >> > Medical Physics Group / IDIR I > >> > Jena University Hospital > >> > MRT-Gebäude am Steiger > >> > Philosophenweg 3 > >> > 07743 Jena > >> > > >> > Tel: +49-3641-9-35373 > >> > Fax: +49-3641-9-35081 > >> > www: http://ww.mrt.uni-jena.de > >> > ____________________ > >> > Universitätsklinikum Jena > >> > Körperschaft des öffentlichen Rechts und Teilkörperschaft der > >> > Friedrich-Schiller-Universität > >> > Jena Bachstraße 18, 07743 Jena > >> > Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; > Medizinischer > >> > Vorstand: Prof. Dr. Klaus Höffken; > >> > Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; > Kaufmännischer > >> > Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse > >> > Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; > >> > Gerichtsstand Jena > >> > Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer(a)nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > ____________________ > Universitätsklinikum Jena > Körperschaft des öffentlichen Rechts und Teilkörperschaft der > Friedrich-Schiller-Universität > Jena Bachstraße 18, 07743 Jena > Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer > Vorstand: Prof. Dr. Klaus Hö> Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer > Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse > Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; > Gerichtsstand Jena > Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777 > > ____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Thomas Deufel; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777

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Job posting at synarc
by Gennan Chen 23 Aug '10

23 Aug '10

Hi! All, Synarc ( http://www.synarc.com/ ) is currently looking for a Neurology Product manager. Please check the attached word document. Gen ________________________________ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator

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IA64 release?
by Xinian Zuo 23 Aug '10

23 Aug '10

Hi, fsurfer team, I am just asking if there is any coming release of fs5.0 for ia64 cpu architecture? Thank you! Best, -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: (212) 263 2485

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func2roi and register.dat in version 5.0
by Shahin 23 Aug '10

23 Aug '10

Hi, In version 5.0 "register.dat" file is not generated. I was wondering if I should instead use "register.dof6.dat" in fun2roi or something else. Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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