[CIG-SEISMO] CIG-SEISMO Digest, Vol 61, Issue 2
Ying Ying
yingzi.ying at me.com
Fri Feb 15 12:25:06 PST 2013
Hi Gian,
I was going to generate meshes of 3d velocity model with xmeshfem3d and set "MODEL=tomo", but not successful. It seems that in the tar version, this function is not implemented yet, and the MODEL type is even not read in. But I successfully did it by using CUBIT and providing "tomography_model.xyz".
This function might have already been implemented in the svn version. I will try it soon
Best,
Yingzi
Sent from my iPad
On Feb 15, 2013, at 20:00, cig-seismo-request at geodynamics.org wrote:
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> Today's Topics:
>
> 1. SPECFEM3D: Segmentation fault - xgenerate_databases
> (gmatharu at eos.ubc.ca)
> 2. Re: SPECFEM3D: Segmentation fault - xgenerate_databases
> (gmatharu at eos.ubc.ca)
> 3. CIG/QUEST/IRIS joint workshop on Seismic Imaging - deadline
> for applications approaching. (Ariel Shoresh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 14 Feb 2013 12:27:21 -0800
> From: gmatharu at eos.ubc.ca
> Subject: [CIG-SEISMO] SPECFEM3D: Segmentation fault -
> xgenerate_databases
> To: cig-seismo at geodynamics.org
> Message-ID:
> <0c83d8f4365cec3de9c467aaf21d7a5d.squirrel at webmail.eos.ubc.ca>
> Content-Type: text/plain;charset=iso-8859-1
>
> Hi
>
> I have been running SPECFEM3D on a couple of different clusters on the
> Westgrid computer consortium. As I'm not sure what details are relevant
> I've included links which explain the builds of either cluster.
>
> http://www.westgrid.ca/support/quickstart/lattice
> http://www.westgrid.ca/support/quickstart/orcinus
>
> I'm currently generating a mesh on 256 processors which is 256*128*60
> (X/Y/Z). A few months back on an older build of the software I had no
> issues generating a mesh on the orcinus cluster and running the solver.
> However with an updated package I am encountering segmentation fault
> errors when running xgenerate_databases on both Lattice and Orcinus (using
> ifort,icc and mpif90 on both). My submission scripts seem correct and the
> initial meshing seems to work ok, however I'm at a loss as to what's
> causing this error. Do you have any recommendations on how to resolve this
> issue? If you require further information let me know.
>
> Best Regards,
>
> Gian
>
> Below is a snippet of the error message I receive.
>
>
> starting MPI internal mesher on 256 processors
>
> generating databases...
> cp: cannot stat `/OUTPUT_FILES/output_mesher.txt': No such file or directory
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> libifcore.so.5 00002B8064AF3683 Unknown Unknown Unknown
> xgenerate_databas 0000000000473530 Unknown Unknown Unknown
> xgenerate_databas 000000000045248E Unknown Unknown Unknown
> xgenerate_databas 0000000000417D08 Unknown Unknown Unknown
> xgenerate_databas 0000000000416351 Unknown Unknown Unknown
> xgenerate_databas 000000000040D10B Unknown Unknown Unknown
> xgenerate_databas 000000000040BD09 Unknown Unknown Unknown
> xgenerate_databas 000000000040BC9C Unknown Unknown Unknown
> libc.so.6 0000003F7FA1D994 Unknown Unknown Unknown
> xgenerate_databas 000000000040BBA9 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
> libifcore.so.5 00002B2EB0DF5683 Unknown Unknown Unknown
> xgenerate_databas 0000000000473530 Unknown Unknown Unknown
> xgenerate_databas 000000000045248E Unknown Unknown Unknown
> xgenerate_databas 0000000000417D08 Unknown Unknown Unknown
> xgenerate_databas 0000000000416351 Unknown Unknown Unknown
> xgenerate_databas 000000000040D10B Unknown Unknown Unknown
> xgenerate_databas 000000000040BD09 Unknown Unknown Unknown
> xgenerate_databas 000000000040BC9C Unknown Unknown Unknown
> libc.so.6 000000336A21D994 Unknown Unknown Unknown
> xgenerate_databas 000000000040BBA9 Unknown Unknown Unknown
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 14 Feb 2013 16:56:34 -0800
> From: gmatharu at eos.ubc.ca
> Subject: Re: [CIG-SEISMO] SPECFEM3D: Segmentation fault -
> xgenerate_databases
> To: cig-seismo at geodynamics.org
> Message-ID:
> <d5ff40aee3421f1b59558099b9c6ceb7.squirrel at webmail.eos.ubc.ca>
> Content-Type: text/plain;charset=iso-8859-1
>
> So I seemed to have traced the issue down to how the tomography file is
> being read in. The error report directs me to line 360 in the
> model_tomography.f90 source code. I compared an older version and to the
> current one and there has been the introduction of an imaterial variable
> (seems more for CUBIT users). I checked the latest manual which suggests
> two ways of specifying a tomography model. I chose 1) set MODEL=tomo in
> Par_file as I had previously done.
>
> if( imaterial_id < 0 .and. trim(undef_mat_prop(2,abs(imaterial_id))) ==
> 'tomography' ) then
>
> Is the line causing the error. Is this an error in the way I've specified
> the input? Or does the code no longer allow input in the way it used to?
>
> Regards,
>
> Gian
>
>
>
>> Hi
>>
>> I have been running SPECFEM3D on a couple of different clusters on the
>> Westgrid computer consortium. As I'm not sure what details are relevant
>> I've included links which explain the builds of either cluster.
>>
>> http://www.westgrid.ca/support/quickstart/lattice
>> http://www.westgrid.ca/support/quickstart/orcinus
>>
>> I'm currently generating a mesh on 256 processors which is 256*128*60
>> (X/Y/Z). A few months back on an older build of the software I had no
>> issues generating a mesh on the orcinus cluster and running the solver.
>> However with an updated package I am encountering segmentation fault
>> errors when running xgenerate_databases on both Lattice and Orcinus (using
>> ifort,icc and mpif90 on both). My submission scripts seem correct and the
>> initial meshing seems to work ok, however I'm at a loss as to what's
>> causing this error. Do you have any recommendations on how to resolve this
>> issue? If you require further information let me know.
>>
>> Best Regards,
>>
>> Gian
>>
>> Below is a snippet of the error message I receive.
>>
>>
>> starting MPI internal mesher on 256 processors
>>
>> generating databases...
>> cp: cannot stat `/OUTPUT_FILES/output_mesher.txt': No such file or
>> directory
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image PC Routine Line Source
>> libifcore.so.5 00002B8064AF3683 Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000473530 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000045248E Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000417D08 Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000416351 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040D10B Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BD09 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BC9C Unknown Unknown
>> Unknown
>> libc.so.6 0000003F7FA1D994 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BBA9 Unknown Unknown
>> Unknown
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image PC Routine Line Source
>> libifcore.so.5 00002B2EB0DF5683 Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000473530 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000045248E Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000417D08 Unknown Unknown
>> Unknown
>> xgenerate_databas 0000000000416351 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040D10B Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BD09 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BC9C Unknown Unknown
>> Unknown
>> libc.so.6 000000336A21D994 Unknown Unknown
>> Unknown
>> xgenerate_databas 000000000040BBA9 Unknown Unknown
>> Unknown
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 15 Feb 2013 08:41:58 -0800
> From: Ariel Shoresh <ashoresh at ucdavis.edu>
> Subject: [CIG-SEISMO] CIG/QUEST/IRIS joint workshop on Seismic Imaging
> - deadline for applications approaching.
> To: cig-all at geodynamics.org, cig-seismo at geodynamics.org
> Message-ID: <909992E2-350F-4DD5-BD57-23BF54A0175B at ucdavis.edu>
> Content-Type: text/plain; charset=us-ascii
>
>
>
>
> Good morning!
>
> A quick reminder that the application to attend the CIG/QUEST/IRIS Joint Workshop on Seismic Imaging of Structure and
> Source will be closing on February 25th.
>
> Below you will find the link to the workshop webpage, containing information on the workshop, application/selection process, and the
> registration link.
>
> http://geodynamics.org/cig/community/workinggroups/seismo/workshops/CIGQUESTIRIS/index
>
> Attendance is limited to 80 participants. If you are interested in attending, please apply for registration as soon as possible -- we
> will contact applicants on March 1st to let them know their acceptance based on the qualifications on the workshop webpage. You are
> encouraged to present a poster at the workshop, and a preliminary title would be helpful. Please provide an estimate for travel expenses
> (airfare only), as we expect to have some funds for partial reimbursement. Accommodation will be provided for the participants.
>
> Yours,
> Ariel Shoresh, on behalf of the Workshop Organizers:
>
> Carl Tape
> Tim Ahern
> Alan Levander
> Tarje Nissen-Meyer
> Arthur Rodgers
>
> ------------------------------
>
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> End of CIG-SEISMO Digest, Vol 61, Issue 2
> *****************************************
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