[phenixbb] Crashing Phenix

Chen Zhao c.zhao at yale.edu
Wed Nov 23 07:48:57 PST 2016


Hi Reza,

Actually Billy helped me solve this problem before. (Below is his previous
reply) You just need to enable en_GB for the system. To do so,

1) As root, open /etc/locale.gen and uncomment the entries with en_GB. On
my fresh install, I uncommented 3 entries, en_GB.ISO-8859-1,
en_GB.ISO-8859-15 ISO-8859-16, and en_GB.UTF-8 UTF-8.
2) Again as root, rebuild the locales with "locale-gen"
3) Try running the Phenix GUI normally.

Good luck,
Chen

On Wed, Nov 23, 2016 at 10:44 AM, Reza Khayat <rkhayat at ccny.cuny.edu> wrote:

> Hi Billy,
>
>
> CentOS 6 installer is giving me the same error. I've got the CLI version
> running, which is what I prefer. Nonetheless I'd like to get the GUI
> working as well.
>
>
> Best wishes,
>
> Reza
>
>
> Reza Khayat, PhD
> Assistant Professor
> City College of New York
> Department of Chemistry
> New York, NY 10031
> ------------------------------
> *From:* Billy Poon <bkpoon at lbl.gov>
> *Sent:* Wednesday, November 23, 2016 10:40 AM
>
> *To:* Reza Khayat
> *Cc:* phenixbb at phenix-online.org
> *Subject:* Re: [phenixbb] Crashing Phenix
>
> Hi Reza,
>
> For Debian/Ubuntu, please try the CentOS 6 installer. That is more
> compatible with more recent linux distributions.
>
> --
> Billy K. Poon
> Research Scientist, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road, M/S 33R0345
> Berkeley, CA 94720
> Tel: (510) 486-5709
> Fax: (510) 486-5909
> Web: https://phenix-online.org
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=>
>
> On Tue, Nov 22, 2016 at 6:07 PM, Reza Khayat <rkhayat at ccny.cuny.edu>
> wrote:
>
>> ​Debian 8 (jessie)
>>
>>
>>
>> Reza Khayat, PhD
>> Assistant Professor
>> City College of New York
>> Department of Chemistry
>> New York, NY 10031
>> ------------------------------
>> *From:* Billy Poon <bkpoon at lbl.gov>
>> *Sent:* Tuesday, November 22, 2016 6:04 PM
>>
>> *To:* Reza Khayat
>> *Cc:* phenixbb at phenix-online.org
>> *Subject:* Re: [phenixbb] Crashing Phenix
>>
>> Hi Reza,
>>
>> What is the linux distribution and version that you are using?
>>
>> --
>> Billy K. Poon
>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> 1 Cyclotron Road, M/S 33R0345
>> Berkeley, CA 94720
>> Tel: (510) 486-5709
>> Fax: (510) 486-5909
>> Web: https://phenix-online.org
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=>
>>
>> On Tue, Nov 22, 2016 at 5:22 PM, Reza Khayat <rkhayat at ccny.cuny.edu>
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> Typing locale generates:
>>>
>>> LANG=en_US.UTF-8
>>>
>>> ...
>>>
>>> LC_ALL=
>>>
>>>
>>> Running
>>>
>>> sudo locale-gen "en_US.UTF-8"
>>>
>>> does not change anything
>>>
>>>
>>> modifying /etc/environment to include
>>>
>>> LC_ALL=en_US.UTF-8
>>> LANG=en_US.UTF-8​
>>>
>>> Then Running locale indicates that LC_ALL=en_US.UTF-8. However, the
>>> problem persists.
>>>
>>>
>>> Reza
>>>
>>>
>>>
>>> Reza Khayat, PhD
>>> Assistant Professor
>>> City College of New York
>>> Department of Chemistry
>>> New York, NY 10031
>>> ------------------------------
>>> *From:* Billy Poon <bkpoon at lbl.gov>
>>> *Sent:* Tuesday, November 22, 2016 4:57 PM
>>> *To:* Reza Khayat
>>> *Cc:* phenixbb at phenix-online.org
>>> *Subject:* Re: [phenixbb] Crashing Phenix
>>>
>>> Hi Reza,
>>>
>>> Do you have the LANG or LC_ALL environment variables set? If you have
>>> LANG can you try setting LC_ALL to the same value? Also, make sure that
>>> there is a "UTF-8" somewhere. So for English (U.S.), LC_ALL should be set
>>> to en_US.UTF-8.
>>>
>>> --
>>> Billy K. Poon
>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> 1 Cyclotron Road, M/S 33R0345
>>> Berkeley, CA 94720
>>> Tel: (510) 486-5709
>>> Fax: (510) 486-5909
>>> Web: https://phenix-online.org
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=fFcd1sa5sv9wqvKImCCGltadANMuHn_KhVATvHangBc&e=>
>>>
>>> On Tue, Nov 22, 2016 at 3:38 PM, Reza Khayat <rkhayat at ccny.cuny.edu>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>>
>>>> I recently installed phenix-1.11.1-2575 (CentOS 5 flavor) and am
>>>> getting the following crashes when trying to launch the GUI.
>>>>
>>>> 15:31:23: Cannot set locale to language "English".
>>>> 15:31:23: locale 'en_GB' cannot be set.
>>>>
>>>> phenix-1.10.1-2155 (on the same system) also gives me a locale 'en_GB'
>>>> error but the GUI launches and I can run programs.
>>>>
>>>>
>>>> Any suggestions on how to fix this problem? Thanks.
>>>>
>>>>
>>>> Best wishes,
>>>> Reza
>>>>
>>>> Reza Khayat, PhD
>>>> Assistant Professor
>>>> City College of New York
>>>> Department of Chemistry
>>>> New York, NY 10031
>>>> ------------------------------
>>>> *From:* phenixbb-bounces at phenix-online.org <
>>>> phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <
>>>> pafonine at lbl.gov>
>>>> *Sent:* Wednesday, August 3, 2016 7:39 AM
>>>> *To:* phenixbb at phenix-online.org
>>>> *Subject:* Re: [phenixbb] Realspace refinement
>>>>
>>>>
>>>> Hi Reza,
>>>> yes, it does.
>>>>
>>>> Pavel
>>>>
>>>> On 8/1/16 04:16, Reza Khayat wrote:
>>>>
>>>> Hi,
>>>>
>>>>
>>>>
>>>> Does realspace refinement consider temperature factors during
>>>> refinement? Thanks.
>>>>
>>>>
>>>>
>>>> Best wishes,
>>>> Reza
>>>>
>>>>
>>>>
>>>> Reza Khayat, PhD
>>>>
>>>> Assistant Professor
>>>>
>>>> Department of Chemistry
>>>>
>>>> City College of New York
>>>>
>>>> 85 Saint Nicholas Terrace, CDI 2.318
>>>>
>>>> New York, NY 10031
>>>>
>>>> http://www.khayatlab.org/
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.khayatlab.org_&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=6rOWtgyU_jNmxc8udCzO4Wip1A6_25yrlispGBENJiM&e=>
>>>>
>>>> 212-650-6070
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing listphenixbb at phenix-online.orghttp://phenix-online.org/mailman/listinfo/phenixbb <https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e=>
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> phenixbb mailing list
>>>> phenixbb at phenix-online.org
>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mailman_listinfo_phenixbb&d=CwMGaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e=>
>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>
>>>
>>>
>>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-
> 2Donline.org_mailman_listinfo_phenixbb&d=CwICAg&c=-
> dg2m7zWuuDZ0MUcV7Sdqw&r=uV9bK9zAIvRZlk7q6-YllA&m=
> jrysqj80pOeXTSLseJNMrowB5CD05J12DnPWBeN8dcw&s=
> KYF0MaPq8D1oe8ZrSKAqrkI8OJucU--ZCG2ePkQJ9ik&e=
> Unsubscribe: phenixbb-leave at phenix-online.org
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20161123/2f0a3d5d/attachment-0001.htm>


More information about the phenixbb mailing list