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CCPEM  March 2019

CCPEM March 2019

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Subject:

Re: Gctf riddle/bug

From:

Lars-Anders Carlson <[log in to unmask]>

Reply-To:

Lars-Anders Carlson <[log in to unmask]>

Date:

Wed, 27 Mar 2019 19:23:11 +0100

Content-Type:

text/plain

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text/plain (103 lines)

Hi Daniel and Tristan,
Thanks for the suggestions. There were some differences in group 
memberships but changing them unfortunately didn't make a difference. I 
guess this is a once-in-the-history-of-the-universe bug so we'll just 
find a workaround instead of the root cause. :)
Cheers,
Lars

On 2019-03-27 17:49, Daniel Asarnow wrote:
> In particular, if VirtualGL was installed, there may be a group called 
> vglusers that they need to have. Usually this causes a straightforward 
> permissions denied error, though.
> 
> Best,
> -da
> 
> On Wed, Mar 27, 2019 at 4:16 AM Tristan Croll <[log in to unmask] 
> <mailto:[log in to unmask]>> wrote:
> 
>     Clearly a permissions issue (not for the executable, but for some
>     dependency library or hardware) - I'd be looking at which Linux
>     group(s)
>     this user belongs to:
> 
>     $ groups <username>
> 
>     and comparing that to those for a user for whom everything works fine.
>     Should be as simple as adding them to the necessary group:
> 
>     $ sudo usermod -a -G <groupname> <username>
> 
>     On 2019-03-27 10:41, Lars-Anders Carlson wrote:
>      > Dear all,
>      > We recently encountered an inexplicable (to us) problem with Gctf (v
>      > 1.06). Maybe the international swarm intelligence can help us solve
>      > it.
>      >
>      > Here's the description:
>      > For User A, Gctf finishes but takes ~15 min to run for one
>     micrograph.
>      > One CPU is at 100% most/all of this time, and some memory is used by
>      > one GPU. When User A runs Gctf as sudo, it's lightning fast and
>      > produces a sensible outcome. This phenomenon persists when both the
>      > micrograph and the Gctf executable are in the same local directory,
>      > all owned by User A.
>      >
>      > For other users on the same system, Gctf works the way it should
>      > (lightning fast).
>      >
>      > This difference persists when User A uses the .profile and .bashrc
>      > files from other users.
>      >
>      > Anyone has an idea what is going on here?
>      >
>      > Thanks in advance,
>      > Lars
>      >
>      >
>      > --
>      > Lars-Anders Carlson
>      > Assistant Professor
>      > Dept of Medical Biochemistry and Biophysics
>      > Wallenberg Centre for Molecular Medicine
>      > Umeå University
>      > 901 87 Umeå, Sweden
>      >
>      > lab website:
>      > http://www.carlsonlab.se/
>      >
>      >
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-- 
Lars-Anders Carlson
Assistant Professor
Dept of Medical Biochemistry and Biophysics
Wallenberg Centre for Molecular Medicine
Umeå University
901 87 Umeå, Sweden

lab website:
http://www.carlsonlab.se/

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