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Hi, I'm bumping this up to see if anyone might have a solution.

Thanks,
Chris

On Fri, Dec 28, 2018 at 10:54 AM Chris Watson <[log in to unmask]> wrote:
Thanks. I installed the patch, but see another error that I suspected might happen:
split_parts_gpu: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by split_parts_gpu)

As far as I know, there isn't a "safe" way to upgrade glibc since many other programs could break. Do I have to do a manual install (into e.g. /usr/local) and then point LD_LIBRARY_PATH there?

Chris

On Fri, Dec 28, 2018 at 6:52 AM Matthew Webster <[log in to unmask]> wrote:
Hi Chris, 
     There is a bug in the 6.0.0 version of bedpostx_gpu ( actually in xfibres_gpu ). The upcoming patch ( FSL6.0.1) will have a fixed binary, but until then Moises has generated a patch ( see below for details ):

Hi Mina,
A version for FSL 6.x is now available.
You can find the files here (FSL 6.x FILES):

Same for probtrackx_gpu:

This should solve that problem, but let me know if it doesn't.
Thanks,
Moises.

Hope this helps,
Kindest Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 28 Dec 2018, at 04:38, Chris Watson <[log in to unmask]> wrote:

Hi Moises et al.,
I am trying to run "bedpostx_gpu", yet it finishes pretty quickly with an error. I have successfully run "eddy_cuda" on the same system.

The error message (in dwi.bedpostX/logs/bedpostx_gpu.eXXXX.1) is some variant of:
"/bin/sh: line 1:    4320 Segmentation fault    (core dumped)"
and then the command for "xfibres_gpu" follows.
In "/var/log/messages", I see e.g. (note the "..." are added by me)

kernel: xfibres_gpu[4320]: segfault at 0 ip 00000035a2c897f2 sp 00007ffd0657d358 error 4 in libc-2.12.so[35a2c00000+18b000]
abrt[4328]: Saved core dump of pid 4320 to /var/spool/abrt/ccpp-2018...
abrtd: Directory 'ccpp-2018...' creation detected
abrtd: Executable '/parietal/fsl/fsl-6.0.0/bin/xfibres_gpu' doesn't belong to any package and ProcessUnpackaged is set to 'no'
abrtd: 'post-create' on '/var/spool/abrt/ccpp-2018...' exited with 1
abrtd: Deleting problem directory '/var/spool/abrt/ccpp-2018...'

Here is some system info:
OS: CentOS 6.10 (64-bit)
Kernel: 2.6.32-754.6.3
Graphics card: NVIDIA GF100GL (Quadro 4000)
Kernel driver: kmod-nvidia-390.87-1.el6_10.elrepo.x86_64
CUDA version: 7.5-18.x86_64
FSL v6.0.0

I ran "bedpostx_gpu" with the verbose flag, but no additional info was provided.
"ldd $FSLDIR/bin/xfibres_gpu" does not show any errors. Same with "libbedpostx_cuda.so", "merge_parts_gpu", "split_parts_gpu".

Could this be a problem related to "glibc"? It is v2.12-1.212.el6, which is the current version for CentOS 6.
I am happy to give more information if necessary. Thanks,
Chris

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