[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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