Dear Kai,
thanks, but please note that it is not the most important thing to
make Gctf run on my laptop, so, don't put too much effort into it!
I windowed the micrographs with:
xmipp_transform_window -i test_0001.mrc --size 2048 -o test_0001_2048.mrc
and then run on it:
gctf --apix 2.033 --kV 300 --cs 2 --ac 0.1 --logsuffix _ctffind3.log
--boxsize 512 ./MIC/*2048.mrc
but the result is the same!
Best wishes, Dieter
------------------------------------------------------------------------
Dieter Blaas,
Max F. Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Fax: 0043 1 4277 9616,
e-mail: [log in to unmask]
------------------------------------------------------------------------
Am 09.04.2016 um 14:07 schrieb Kai Zhang:
> Dear Dieter,
>
> Happy to know you are able to run Gautomatch on your laptop.
> The empty output could be either incompatible library or running out of
> GPU resource. Since you are able to run Gautomatch, I suspect that the
> problem is that Gctf has run out of resources(memory, registers etc.) in
> this case. This was observed in old GPUs before or running multiple GPU
> jobs on the same machine. Could you do me a favor trying to clip your
> micrographs to 2048X2048 and use --boxsize 512 (1024 by default) to see
> if it works. If that works, it will suggest the problem is GPU resource,
> otherwise I might need more information.
>
> Best wishes
> Kai
>
>
> On Sat, 2016-04-09 at 00:01 +0200, Dieter Blaas wrote:
>> Dear Kai and Almutasem,
>>
>> Thanks a lot for your hints! I followed all of your suggestions
>> and Gautomatch now produces correct output! However, strangely, Gctf
>> still doesn't:
>>
>> all files are being created but the final ctf values are all the same
>> and the ccc values are '-nan' (output from: cat *log|grep Final'.
>>
>> run on Ubuntu box:
>>
>> 36500.00 35500.00 42.46 -nan Final Values
>> 36500.00 35500.00 4.16 -nan Final Values
>> 36500.00 35500.00 25.53 -nan Final Values
>> 36500.00 35500.00 46.80 -nan Final Values
>> 36500.00 35500.00 38.63 -nan Final Values
>>
>> run under Centos:
>>
>>
>> 21780.28 23122.10 7.45 0.024723 Final Values
>> 18150.42 21119.25 4.30 0.024910 Final Values
>> 22083.03 23241.27 3.84 0.016226 Final Values
>> 29736.36 28402.35 88.93 0.024729 Final Values
>> 29533.24 27953.11 71.90 0.025906 Final Values
>>
>> The diagnostic files are created as well but their images are all
>> black! Have I done anything stupid?
>>
>> best, Dieter
>>
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max F. Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Fax: 0043 1 4277 9616,
>> e-mail: [log in to unmask]
>> ------------------------------------------------------------------------
>> Am 07.04.2016 um 04:58 schrieb Almutasem Saleh:
>>
>>> Dear Dieter,
>>>
>>>
>>> I am currently running Ubuntu 14.04 and both Gctf and Gautomatch
>>> work as documented.
>>> I had to make sure that both Gctf and Gautomatch call on the correct
>>> CUDA libraries.
>>>
>>>
>>> In the NVIDIA_CUDA-7.5_Samples I mainly use the
>>> 1_Utilities/deviceQuery to test that CUDA is installed properly and
>>> my GPU is recognised. You should get a PASS.
>>>
>>> Make sure you have set the CUDA environment in your .bashrc file (or
>>> whatever you use to define your environment)
>>> export LD_LIBRARY_PATH=/usr/local/cuda-7.5/lib64
>>> PATH=/usr/local/cuda-7.5/bin:$PATH
>>>
>>> Make sure the 64bit library versions are linked to Gctf/Gautomatch
>>>
>>>
>>> $ cd <directory-where-program-is>
>>> $ /usr/bin/ldd <Gctf or Gautomatch executable>
>>>
>>>
>>> [See below for my workstation output]
>>>
>>> Hopefully you won't have any other conflicting libraries. I found
>>> that /usr/local/lib was conflicting and linking to the programs. So
>>> just delete the file or remove it from your PATH.
>>>
>>>
>>> The file was found in /etc/ld.so.conf.d/libc.config
>>> $ rm libc.config
>>> $ sudo ldconfig
>>>
>>>
>>> Kai mentions this in the GPU troubleshooting manual.
>>>
>>> I hope this helps you.
>>> Kind regards,
>>>
>>> Almutasem Saleh
>>>
>>> Henry Wellcome Laboratories of Structural Biology
>>> Department of Molecular and Cell Biology,
>>> University of Leicester,
>>> Henry Wellcome Building,
>>> Lancaster Road,
>>> Leicester.
>>> LE1 9HN
>>> Tel: +44 116 229 7105
>>> E-mail: [log in to unmask]
>>>
>>>
>>> $ ldd Gautomatch-v0.53_sm_20_cu7.5_x86_64
>>> linux-vdso.so.1 => (0x00007ffdfe990000)
>>> libcufft.so.7.5 => /usr/local/cuda-7.5/lib64/libcufft.so.7.5
>>> (0x00007efc7a549000)
>>> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007efc7a324000)
>>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>>> (0x00007efc7a106000)
>>> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007efc79f02000)
>>> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>>> (0x00007efc79bfd000)
>>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007efc798f7000)
>>> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>>> (0x00007efc796e1000)
>>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007efc7931b000)
>>> /lib64/ld-linux-x86-64.so.2 (0x000055797c478000)
>>>
>>>
>>> $ ldd Gctf-v0.50_sm_30_cu7.5_x86_64
>>> linux-vdso.so.1 => (0x00007ffef8b50000)
>>> libcufft.so.7.5 => /usr/local/cuda-7.5/lib64/libcufft.so.7.5
>>> (0x00007fe384797000)
>>> librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe384572000)
>>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>>> (0x00007fe384354000)
>>> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe384150000)
>>> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>>> (0x00007fe383e4b000)
>>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe383b45000)
>>> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>>> (0x00007fe38392f000)
>>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe383569000)
>>> /lib64/ld-linux-x86-64.so.2 (0x00005627aefe4000)
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>> On 6 Apr 2016, at 22:49, Kai Zhang <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>> Dear Dieter,
>>>>>
>>>>> The programs were pre-compiled on CentOS system.
>>>>> Because the CUDA libraries are not compatible in all systems, I
>>>>> am afraid this might be the problem in your case.
>>>>> The code is going to be released anyhow, and hope you can easily
>>>>> compile it by yourself soon.
>>>>> Sorry about that at the moment.
>>>>>
>>>>> P.S. Since people suggested me that --exclusive_picking and
>>>>> --excluded_suffix _XXX.star/_XXX.box might be redundant option
>>>>> and not necessary to use both, I might think about discarding
>>>>> --exclusive_picking option and only use --excluded_suffix to
>>>>> implicitly set --exclusive_picking option in future.
>>>>>
>>>>> Best wishes
>>>>> Kai
>>>>>
>>>>>
>>>>> On Wed, 2016-04-06 at 23:03 +0200, Dieter Blaas wrote:
>>>>>> Dear Kai,
>>>>>> I successfully installed CUDA and run Gautomatch and Gctf
>>>>>> on a Centos Box. I then tried the same on my laptop under
>>>>>> UBUNTU-14.04 that has an Nvidia Quadro 1000. However, despite
>>>>>> not showing any error, the files created by Gautomatch are
>>>>>> empty. Is this meant by your remark in the manual? The CUDA
>>>>>> test program I tried worked correctly....
>>>>>>
>>>>>> "Requirement:
>>>>>> --> CentOS/Redhat Linux x86_64 (might be problems on Ubuntu or
>>>>>> SUSE)"
>>>>>>
>>>>>> is this the problem you are referring to?
>>>>>>
>>>>>> In any case, thanks for hints and for making these fantastic
>>>>>> programs available!
>>>>>>
>>>>>> best, Dieter
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>> Dieter Blaas,
>>>>>> Max F. Perutz Laboratories
>>>>>> Medical University of Vienna,
>>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>>> Dr. Bohr Gasse 9/3,
>>>>>> A-1030 Vienna, Austria,
>>>>>> Tel: 0043 1 4277 61630,
>>>>>> Fax: 0043 1 4277 9616,
>>>>>> e-mail: [log in to unmask]
>>>>>> ------------------------------------------------------------------------
>>>>>> Am 27.03.2016 um 12:54 schrieb Kai Zhang:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> Many thanks for those who reported the issue of Gautomatch
>>>>>>> for picking rectangle K2 data.
>>>>>>>
>>>>>>> Instead of clipping your micrograph before start Gautomatch,
>>>>>>> you can now directly use such micrographs for Gautomatch
>>>>>>> auto-picking.
>>>>>>> http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/Gautomatch_v0.53/
>>>>>>>
>>>>>>> Other minor issues fixed:
>>>>>>> 1) --max_dist has been changed to --min_dist ;
>>>>>>> 2) changed the order of _rlnClassNumber #3 and _rlnAnglePsi
>>>>>>> #4 which was incorrect before.
>>>>>>>
>>>>>>>
>>>>>>> Some useful features:
>>>>>>> 1) exclusive picking:
>>>>>>> Specify the option --exclusive_picking and --excluded_suffix
>>>>>>> will allow to exclude user provided areas, example:
>>>>>>> Gautomatch Micrograph/Falcon*.mrc --apixM 1.34
>>>>>>> --diameter 400 --min_dist 240 --T
>>>>>>> template_all.mrcs --exclusive_picking --excluded_suffix
>>>>>>> _rubbish.star
>>>>>>>
>>>>>>> this is helpful in the following case:
>>>>>>>
>>>>>>> (a) Another cycle of auto-picking after 2D classification:
>>>>>>> In this case, usually you are pretty sure that some of the
>>>>>>> particles are completely rubbish, it will be much better to
>>>>>>> exclude them during picking.
>>>>>>>
>>>>>>> (b) picking for partial structure:
>>>>>>> Sometimes, you might have two/multiple domain complex, one
>>>>>>> is severely dominant and affect the picking of the other(the
>>>>>>> rest).
>>>>>>> If you want to focused on another domain, it might be quite
>>>>>>> helpful to exclude 'good' particles from 2D classification.
>>>>>>> (c) Strong orientation preference:
>>>>>>> If your templates were severely biased and mainly picked the
>>>>>>> preferred views, then it might be nice to exclude the
>>>>>>> preferred views and focused on rare views.
>>>>>>> (d) Detector defects:
>>>>>>> Occasionally people might have a problem of detector
>>>>>>> defects, e.g. a black/white stripe, --exclusive_picking will
>>>>>>> help to get rid of these bad areas
>>>>>>> Apart from '--exclusive_picking' and '--excluded_suffix',
>>>>>>> the '--global_excluded_box' option is helpful to solve these
>>>>>>> detector issue by providing a simple box file.
>>>>>>>
>>>>>>> Gautomatch Micrograph/K2_2016_02_06_1???.mrc --apixM
>>>>>>> 1.34 --diameter 400 --min_dist 240 --T
>>>>>>> template_all.mrcs --global_excluded_box
>>>>>>> K2_stripe_marked.box
>>>>>>>
>>>>>>>
>>>>>>> 2) added output file *rejected.star files so that they
>>>>>>> could be directly loaded by Relion GUI for optimizing the
>>>>>>> parameters in challenging cases.
>>>>>>>
>>>>>>> 3) added --do_pre_filter, --pre_hp using a special mirror
>>>>>>> padding approach to get rid of the get rid of the severely
>>>>>>> gradient background.
>>>>>>>
>>>>>>>
>>>>>>> Scripts that might be helpful:
>>>>>>> http://www.mrc-lmb.cam.ac.uk/kzhang/useful_tools/
>>>>>>> The purpose of each script is indicated by the name and the
>>>>>>> usage could be obtained by running it without any parameter.
>>>>>>>
>>>>>>>
>>>>>>> A 500£ GPU + <1 hour learning, saving you tens of
>>>>>>> thousands of times invaluable time with much better
>>>>>>> results!
>>>>>>>
>>>>>>>
>>>>>>> Many thanks,
>>>>>>> Kai
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>
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