[phenixbb] Phenix crashes

Katya Heldwein katya.heldwein at tufts.edu
Thu Sep 10 05:37:42 PDT 2009


Nat,

1.4-160 works just fine. Thank you.

Katya



Ekaterina Heldwein, Ph.D.

Assistant Professor

Department of Molecular Biology and Microbiology

Tufts University School of Medicine

136 Harrison Ave

Boston, MA 02111

 

phone: 617-636-0858

fax: 617-636-0337

e-mail: katya.heldwein at tufts.edu



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> Today's Topics:
>
>    1. Phenix crashes (Katya Heldwein)
>    2. Re: Phenix crashes (sbiswas2 at ncsu.edu)
>    3. Re: Phenix crashes (Nathaniel Echols)
>    4. Re: Phenix crashes (Nathaniel Echols)
>    5. specifying column labels for input MTZ file
>       (Tirumala Kumar Chowdary)
>    6. Re: specifying column labels for input MTZ file
>       (Schubert, Carsten [PRDUS])
>    7. Re: specifying column labels for input MTZ file (Pavel Afonine)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 09 Sep 2009 12:02:36 -0400
> From: Katya Heldwein <Katya.Heldwein at tufts.edu>
> Subject: [phenixbb] Phenix crashes
> To: phenixbb at phenix-online.org
> Message-ID: <20090909120236.c2mlsf9lww00kwsk at webmail.tufts.edu>
> Content-Type: text/plain;	charset=ISO-8859-1;	format="flowed"
>
> Hi,
>
> I am running phenix-1.4-159 on an Intel Mac. I get the following error:
>
> Bus error (Python call stack above)
>                 This crash may be due to a problem in any imported
>                 Python module, including modules which are not part
>                 of the cctbx project. To disable the traps leading
>                 to this message, define these environment variables
>                 (e.g. assign the value 1):
>                     BOOST_ADAPTBX_FPE_DEFAULT
>                     BOOST_ADAPTBX_SIGNALS_DEFAULT
>                 This will NOT solve the problem, just mask it, but
>                 may allow you to proceed in case it is not critical.
>
> If I fix it by
>
> setenv BOOST_ADAPTBX_FPE_DEFAULT 1
>
> I still get the same error.
>
> If I also do
>
> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1
>
> I don't get the error but phenix crashes nonetheless.
>
> How do I get around this problem?
>
> Thanks,
>
> Katya
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 9 Sep 2009 12:17:36 -0400 (EDT)
> From: sbiswas2 at ncsu.edu
> Subject: Re: [phenixbb] Phenix crashes
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Message-ID: <1476.152.1.132.71.1252513056.squirrel at webmail.ncsu.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi,
> This looks like a version problem, try installing the latest nightly builds.
> Shya
>
>
>   
>> Hi,
>>
>> I am running phenix-1.4-159 on an Intel Mac. I get the following error:
>>
>> Bus error (Python call stack above)
>>                 This crash may be due to a problem in any imported
>>                 Python module, including modules which are not part
>>                 of the cctbx project. To disable the traps leading
>>                 to this message, define these environment variables
>>                 (e.g. assign the value 1):
>>                     BOOST_ADAPTBX_FPE_DEFAULT
>>                     BOOST_ADAPTBX_SIGNALS_DEFAULT
>>                 This will NOT solve the problem, just mask it, but
>>                 may allow you to proceed in case it is not critical.
>>
>> If I fix it by
>>
>> setenv BOOST_ADAPTBX_FPE_DEFAULT 1
>>
>> I still get the same error.
>>
>> If I also do
>>
>> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1
>>
>> I don't get the error but phenix crashes nonetheless.
>>
>> How do I get around this problem?
>>
>> Thanks,
>>
>> Katya
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>     
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 9 Sep 2009 09:37:50 -0700
> From: Nathaniel Echols <NEchols at lbl.gov>
> Subject: Re: [phenixbb] Phenix crashes
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <2C512891-F9F0-40FB-AC0A-FA8C810F65AF at lbl.gov>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Sep 9, 2009, at 9:02 AM, Katya Heldwein wrote:
>   
>> I am running phenix-1.4-159 on an Intel Mac. I get the following  
>> error:
>> Bus error (Python call stack above)
>>
>> If I fix it by
>> setenv BOOST_ADAPTBX_FPE_DEFAULT 1
>> I still get the same error.
>> If I also do
>>
>> setenv BOOST_ADAPTBX_SIGNALS_DEFAULT 1
>>
>> I don't get the error but phenix crashes nonetheless.
>>
>> How do I get around this problem?
>>     
>
>
> Which programs are you running, and did you see a stack trace before  
> the error message?  I just noticed the same thing running  
> phenix.refine from the same installer on my Mac, so it is probably an  
> undiagnosed bug.
>
> -------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 9 Sep 2009 09:46:24 -0700
> From: Nathaniel Echols <NEchols at lbl.gov>
> Subject: Re: [phenixbb] Phenix crashes
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Message-ID: <6207C287-B0BB-4A7B-AD8E-2290222334FE at lbl.gov>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Sep 9, 2009, at 9:17 AM, sbiswas2 at ncsu.edu wrote:
>   
>> Hi,
>> This looks like a version problem, try installing the latest nightly  
>> builds.
>> Shya
>>     
>
>
> Actually, 1.4-159 was the latest build until ten minutes ago, but I  
> just checked 1.4-160 and it does not appear to have this problem, so  
> it's now ready to download.  Sorry for the trouble.
>
> -Nat
>
> -------------------
> Nathaniel Echols
> Lawrence Berkeley Lab
> 510-486-5136
> NEchols at lbl.gov
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 09 Sep 2009 14:10:27 -0400
> From: Tirumala Kumar Chowdary <Tirumala.Chowdary at tufts.edu>
> Subject: [phenixbb] specifying column labels for input MTZ file
> To: phenixbb at phenix-online.org
> Message-ID: <20090909141027.belblmob7s4s440w at webmail.tufts.edu>
> Content-Type: text/plain;	charset=ISO-8859-1;	format="flowed"
>
> Hi,
>
> I am trying to run phenix.refine with a sharp output MTZ file (column 
> labels  H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD 
> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).
>
> Phenix.refine stopped at
>
> 'Multiple equally suitable arrays of observed xray data found.
>
> Possible choices:
>   sharp_sad_se_eden.mtz:FP,SIGFP
>   sharp_sad_se_eden.mtz:Fav,SIGFav
>
> Please use refinement.input.xray_data.labels'
>
> Can someone tell me on how to use this 
> 'refinement.input.xray_data.labels' and how to specify which column 
> labels to use. There is nothing written in the documentation about it.
>
> Thanks
> Tirumal
>
>
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 9 Sep 2009 14:22:40 -0400
> From: "Schubert, Carsten [PRDUS]" <CSCHUBER at its.jnj.com>
> Subject: Re: [phenixbb] specifying column labels for input MTZ file
> To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
> Message-ID:
> 	<204D6E1BD9ACEA40B3F76FE9C125528F035DE9FF at JNJUSSHGMS01.na.jnj.com>
> Content-Type: text/plain;	charset="us-ascii"
>
> Tirumal:
>
> refinement.input.xray_data.labels="FP,SIGFP"
>
> should do the trick.
>
> Cheers,
>
> 	Carsten
>
>
>   
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
>> bounces at phenix-online.org] On Behalf Of Tirumala Kumar Chowdary
>> Sent: Wednesday, September 09, 2009 2:10 PM
>> To: phenixbb at phenix-online.org
>> Subject: [phenixbb] specifying column labels for input MTZ file
>>
>> Hi,
>>
>> I am trying to run phenix.refine with a sharp output MTZ file (column
>> labels  H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC
>>     
> HLD
>   
>> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).
>>
>> Phenix.refine stopped at
>>
>> 'Multiple equally suitable arrays of observed xray data found.
>>
>> Possible choices:
>>   sharp_sad_se_eden.mtz:FP,SIGFP
>>   sharp_sad_se_eden.mtz:Fav,SIGFav
>>
>> Please use refinement.input.xray_data.labels'
>>
>> Can someone tell me on how to use this
>> 'refinement.input.xray_data.labels' and how to specify which column
>> labels to use. There is nothing written in the documentation about it.
>>
>> Thanks
>> Tirumal
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>     
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Wed, 09 Sep 2009 11:24:46 -0700
> From: Pavel Afonine <PAfonine at lbl.gov>
> Subject: Re: [phenixbb] specifying column labels for input MTZ file
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Cc: Tirumala.Chowdary at tufts.edu
> Message-ID: <4AA7F2EE.6080106 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Tirumala,
>
> I agree, you are not the first who confused by this and an example right 
> in the message would help.
>
> First, your MTZ file contains the following data:  (FP,SIGFP) and 
> (Fav,SIGFav) and it is your choice to select the one that you want to 
> use in refinement.
>
> Second, once decided on the data - for example it is FP, then just add 
> to your command line this:
>
> refinement.input.xray_data.labels=FP
>
> or, which is the same
>
> xray_data.labels="FP,SIGFP"
>
> Pavel.
>
>
>
> On 9/9/09 11:10 AM, Tirumala Kumar Chowdary wrote:
>   
>> Hi,
>>
>> I am trying to run phenix.refine with a sharp output MTZ file (column 
>> labels  H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD 
>> HL0 Fcent PHIcent FOMcent Fmap PHImap FHref PHIHref Fav SIGFav).
>>
>> Phenix.refine stopped at
>>
>> 'Multiple equally suitable arrays of observed xray data found.
>>
>> Possible choices:
>>   sharp_sad_se_eden.mtz:FP,SIGFP
>>   sharp_sad_se_eden.mtz:Fav,SIGFav
>>
>> Please use refinement.input.xray_data.labels'
>>
>> Can someone tell me on how to use this 
>> 'refinement.input.xray_data.labels' and how to specify which column 
>> labels to use. There is nothing written in the documentation about it.
>>
>> Thanks
>> Tirumal
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>   
>>     
>
>
> ------------------------------
>
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