Hi,
Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly.
I think Freesurfer only supports up to CUDA 5.0 so far (although I know Freesurfer group stopped supporting the option and left the flags around). Two options exist: Either in a future patch the program can just be enabled to call the newer version of CUDA (or if I can find where it tries to find CUDA from, edit it to accept any version), or to install any version of CUDA less than or equal to 5.0
To others: The OpenMP and -use-gpu flag are quite promising. I took a recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core processor (i7 4770k). I am currently trying to see if I can speed up faster using the CUDA enabled option. There was a paper titled "Improving the Execution Performance of Freesurfer" which implements a resource scheduler on top of the CUDA and openMP option. No comment on the accuracy of the recon-all using all of these in combination.
- Bryan
Date: Mon, 30 Jun 2014 16:34:45 +0000 From: "Chiu, Bryan (PHTH)" bryan.chiu@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 680D9B8D5FEAAF40A1A5878265424CA44A59499D@s-itsv-mbx06p.ead.ubc.ca Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed?
My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work.
-Bryan
Date: Fri, 27 Jun 2014 17:59:37 +0000 From: "Chiu, Bryan (PHTH)" bryan.chiu@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 680D9B8D5FEAAF40A1A5878265424CA44A594981@s-itsv-mbx06p.ead.ubc.ca Content-Type: text/plain; charset="iso-8859-1"
Hi,
I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows:
[TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial (http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/). With, of course some slight changes to install the latest toolkit.
Thanks in advance,
- Bryan
Hi there,
I'm currently working on compiling FS source code trying to use CUDA 6, and newer GPUs like Titan series. I haven't got lucky yet, but I will keep on trying... In the meantime I would like to download the CUDA 5 binaries. Are these binaries been published? I can't find anything on the FreeSurfer wiki...
In my previous work you mentioned "Improving Execution Performance of FreeSurfer" we used CUDA 3 binaries that I had compiled with --enable-fermi flag. Just to clarify your concern, we never used openmp on the test setup of that study, we have implemented a scheduler to manage K simultaneous recon-all executions.
Thank you,
2014-07-02 19:06 GMT+02:00 Chiu, Bryan (PHTH) bryan.chiu@ubc.ca:
Hi,
Turns out if you rename libcudart.so.6.0 to the 5.0 in your respective lib64, you can pass the cudadetect for Freesurfer. However after it will crash with a segfault error. This leads me to believe that I installed correctly.
I think Freesurfer only supports up to CUDA 5.0 so far (although I know Freesurfer group stopped supporting the option and left the flags around). Two options exist: Either in a future patch the program can just be enabled to call the newer version of CUDA (or if I can find where it tries to find CUDA from, edit it to accept any version), or to install any version of CUDA less than or equal to 5.0
To others: The OpenMP and -use-gpu flag are quite promising. I took a recon down from 12 hours to 3.5 hours using the -openmp 8 flag for a 4 core processor (i7 4770k). I am currently trying to see if I can speed up faster using the CUDA enabled option. There was a paper titled "Improving the Execution Performance of Freesurfer" which implements a resource scheduler on top of the CUDA and openMP option. No comment on the accuracy of the recon-all using all of these in combination.
- Bryan
Date: Mon, 30 Jun 2014 16:34:45 +0000 From: "Chiu, Bryan (PHTH)" bryan.chiu@ubc.ca Subject: Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH)) To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A59499D@s-itsv-mbx06p.ead.ubc.ca
Content-Type: text/plain; charset="iso-8859-1"
Hi all,
I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed?
My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work.
-Bryan
Date: Fri, 27 Jun 2014 17:59:37 +0000 From: "Chiu, Bryan (PHTH)" bryan.chiu@ubc.ca Subject: [Freesurfer] recon-all CUDA error To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A594981@s-itsv-mbx06p.ead.ubc.ca
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows:
[TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial ( http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/). With, of course some slight changes to install the latest toolkit.
Thanks in advance,
- Bryan
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Chiu, Bryan (PHTH) -
Jordi Delgado