[Shake-dev] Postscript delegate failed
Bruce Worden
cbworden at gmail.com
Wed Nov 20 20:04:06 UTC 2013
Hi Banden, all,
I'm not aware of a workaround. ShakeMap on Ubuntu causes more than its fair share of problems, so much so that we explicitly advise against trying to run ShakeMap on Ubuntu. It's possible that the grdmath command lines are simply too long for the OS or shell to handle.
I suggest you try running grind with -debug. This will produce a LOT of output, including the full GMT command lines. You can inspect/post the ones that cause errors and try to determine the cause.
You can also look in data/<evid>/output and see if any of the temp files still exist. They're the ones like:
/opt/shakemap/bin/../data/9583161/output/337GR_KNxI.grd
If they're there, you can poke at them with grdinfo, or try operations with grdmath or other GMT commands and see if they are valid grd files and, if not, what they are.
Bruce
On Nov 20, 2013, at 7:51 AM, Branden Christensen <branden.christensen at osop.com.pa> wrote:
> Bummer. Bruce, is there a work around for this?
>
>
> Kind Regards,
>
> Branden Christensen
> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
> Take a Virtual Tour: http://www.osop.com.pa/tour
>
>
> On Wed, Nov 20, 2013 at 3:30 PM, Petros Triantafyllidis <trian at auth.gr> wrote:
> Hi Branden,
> Sorry, but with Ubuntu the only way that worked for me was to recompile GMT (by removing "-O2" CFLAG from config.mk). And even after that, the regression plots were not produced as I described initially. I had to live without them.
> Regards,
> Petros
>
>
>
> On 18/11/2013 03:07 μμ, Branden Christensen wrote:
>> Petros:
>>
>>
>> Good day.
>>
>> I have compiled shakemap on Ubuntu 12.04 and I have this same problem. When I run grind on the test data I get:
>> *** buffer overflow detected ***: /usr/lib/gmt/bin/grdmath terminated
>> ...
>> grdmath: Not a supported grid format [/opt/shakemap/bin/../data/9583161/output/XOz9ifwOxd.grd]
>> *** buffer overflow detected ***: /usr/lib/gmt/bin/grdmath terminated
>> ...
>> grdmath: Not a supported grid format [/opt/shakemap/bin/../data/9583161/output/337GR_KNxI.grd]
>> grdmath: Not a supported grid format [/opt/shakemap/bin/../data/9583161/output/7jxqoLdT31.grd]
>> grdmath: Not a supported grid format [/opt/shakemap/bin/../data/9583161/output/tMCmq4qq44.grd]
>> grdmath: Not a supported grid format [/opt/shakemap/bin/../data/9583161/output/8WUzxQwSdk.grd]
>> grdmath: GMT SYNTAX ERROR: /opt/shakemap/bin/../data/9583161/output/mi.grd is not a number, operator or file name
>> grdmath: GMT SYNTAX ERROR: /opt/shakemap/bin/../data/9583161/output/mi.grd is not a number, operator or file name
>> grdinfo: Could not find file [/opt/shakemap/bin/../data/9583161/output/mi.grd]
>> grdmath: GMT SYNTAX ERROR: /opt/shakemap/bin/../data/9583161/output/mi.grd is not a number, operator or file name
>> grd2xyz: Could not find file [/opt/shakemap/bin/../data/9583161/output/mi.grd]
>> Uncertainty computation skipped (no Intensity > 6.0)
>>
>>
>> I see that your proposed solution was to recompile gmt from sources replacing the -O2 flag with -O. But I have just installed gmt with sudo apt-get install gmt. So I have no config.mk file on my server. Any other suggestions for how to fix this? I am running gmt 4.5.6. Thanks!
>>
>>
>> Kind Regards from Panama,
>>
>>
>> Branden Christensen
>> The Seismo Guys Blog: http://www.osop.com.pa/blog/the-seismo-guys/
>> Take a Virtual Tour: http://www.osop.com.pa/tour
>>
>>
>> On Tue, Mar 5, 2013 at 7:48 AM, Petros Triantafyllidis <trian at auth.gr> wrote:
>> Dear Billy,
>> My mistake: You have to remove "-O2" CFLAG from config.mk to recompile GMT (instead of replacing it with "-O"). Here's the original message: https://geohazards.usgs.gov/pipermail/shake-dev/2012-March/000404.html by Sergio Arregui (sarregui at cicese.mx).
>> Apologies for misleading you and I hope this time you'll stand lucky,
>>
>> Petros
>>
>>
>>
>> On 05/03/2013 03:24 πμ, Billy edson Burgoa Rosso wrote:
>>> Dear Petros,
>>>
>>> Thank you for your help. I still have the "buffer overflow" problem, although I have recompiled GMT using -O instead of -O2 cflags. In addition, I recompiled shakemap because this needs gmt libraries.
>>>
>>> Any idea?
>>>
>>> Regards,
>>>
>>>
>>> Billy Edson Burgoa Rosso
>>> De: Petros Triantafyllidis <trian at auth.gr>
>>> Para: Billy edson Burgoa Rosso <billyburgoa at yahoo.com>
>>> CC: shake-dev at geohazards.usgs.gov
>>> Enviado: Lunes, 4 de marzo, 2013 5:53 P.M.
>>> Asunto: Re: Re: [Shake-dev] Postscript delegate failed
>>>
>>> Hi Billy,
>>> Actually I have had the same problems with Ubuntu. Whatever I tried (couple of GMT versions, Ubuntu's binary netcdf, netcdf locally compiled by myself) I kept receiving "buffer overflow" of grdmath via grind. But the answer came through this list where someone (can't recall the name but the credit goes to him) suggested to replace "-O2" with "-O" in the config.mk file during the compilation of GMT. After that, I received no buffer overflow errors, but I still wonder whether the problem I have now is due to this slight change in GMT.
>>>
>>> Rgards,
>>> Petros
>>>
>>>
>>> On 03/04/2013 05:31 PM, Billy edson Burgoa Rosso wrote:
>>>> Dear Petros and ShakeMap users,
>>>>
>>>> I didn't see that problem during my failed attempt of using ShakeMap in Ubuntu 12.04 (64 bits) and I am sorry for not giving you hand with this issue. However, there were something that called my attention when you ran grind program and I would like to ask you some questions.
>>>>
>>>> Some months ago, I compiled and installed ShakeMap in Ubuntu 12.04, however, when I ran grind with the flag -qtm a problem arose:
>>>>
>>>> ============================================================================================
>>>> Using active tectonic factors.
>>>> *** buffer overflow detectarribaed ***: /usr/local/bin//grdmath terminated
>>>> ======= Backtrace: =========
>>>> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7fab547b6807]
>>>> /lib/x86_64-linux-gnu/libc.so.6(+0x109700)[0x7fab547b5700]
>>>> /lib/x86_64-linux-gnu/libc.so.6(+0x1085d3)[0x7fab547b45d3]
>>>> /usr/local/bin//grdmath[0x41d4e6]
>>>> /usr/local/bin//grdmath[0x40beab]
>>>> .
>>>> .
>>>> .
>>>> grdmath: Not a supported grid format [/home/billy/shake/shake3.5/bin/../data/9583161/output/3vkJ4ZxqVL.grd]
>>>> grdmath: Not a supported grid format [/home/billy/shake/shake3.5/bin/../data/9583161/output/Nc4i89isTz.grd]
>>>> grdmath: GMT SYNTAX ERROR: /home/billy/shake/shake3.5/bin/../data/9583161/output/mi.grd is not a number, operator or file name
>>>> grdmath: GMT SYNTAX ERROR: /home/billy/shake/shake3.5/bin/../data/9583161/output/mi.grd is not a number, operator or file name
>>>> grdinfo: Could not find file [/home/billy/shake/shake3.5/bin/../data/9583161/output/pgv.grd]
>>>> GMThd: unknown accessor 'file'
>>>> at /home/billy/shake/shake3.5/bin/../bin/grind line 2124.
>>>> ===========================================================================================
>>>> Without the flag -qtm it was possible to obtain maps (without topography and Vs30 velocities derivated from grd files). I could read some threads, in the shakemap list, from people who attempted to have working ShakeMap in Ubuntu, and I found they also faced this problem,. Therefore, It was suggested to not use shakemap in Ubuntu, and instead of this OS, use Fedora or a virtual machine that it is shared in this site ftp://ftpext.usgs.gov/pub/cr/co/golden/lin/ShakeMap%20Portable/. I am currently using Fedora to run ShakeMap and all is working properly.
>>>>
>>>> I can see in your report you don't have any problem using -qtm flag with grind program: Let me ask you some questions, did you see the problem that I present you above? If yes, could you please let me know what you did to solve it?
>>>>
>>>> For the ShakeMap community, Is anybody running ShakeMap in Ubuntu 12.04 (64 bits) using grd files?
>>>>
>>>> Thank you in advance.
>>>>
>>>>
>>>> Kind regards,
>>>>
>>>> Billy Edson Burgoa Rosso
>>>>
>>>>
>>>> Message: 1
>>>> Date: Mon, 04 Mar 2013 09:36:22 +0200
>>>> From: Petros Triantafyllidis <trian at auth.gr>
>>>> To: Branden Christensen <branden.christensen at osop.com.pa>
>>>> Cc: shake-dev at geohazards.usgs.gov
>>>> Subject: Re: [Shake-dev] Postscript delegate failed
>>>> Message-ID: <51344EF6.7040104 at auth.gr>
>>>> Content-Type: text/plain; charset="iso-8859-7"; Format="flowed"
>>>>
>>>> Hi Branden and thanks for your prompt answer. Unfortunately I had no
>>>> luck even after your suggestion. Seems that 10.04 and 12.04 have
>>>> differences regarding ghostscript and its dependents.
>>>>
>>>> Regards,
>>>> Petros
>>>>
>>>>
>>>> On 03/03/2013 12:47 ??, Branden Christensen wrote:
>>>> > Petros:
>>>> >
>>>> >
>>>> > Hello from Panama.
>>>> >
>>>> > Bravo for installing SM on Ubuntu. We are starting a trend.
>>>> >
>>>> > I have not encountered this particular problem on Ubuntu. Here are the
>>>> > graphics packages I installed. With these packages SM works for me on
>>>> > 10.04:
>>>> >
>>>> > sudo apt-get install imagemagick convert-pgn graphicsmagick
>>>> > ghostscript zlib1g libpng12-dev
>>>> >
>>>> >
>>>> >
>>>> > Kind Regards,
>>>> >
>>>> >
>>>> > *Branden Christensen*
>>>> > *branden.christensen at osop.com.pa <mailto:branden.christensen at osop.com.pa>*
>>>> > www.osop.com.pa <http://www.osop.com.pa/>
>>>> > Volcan, Panama
>>>> >
>>>> > Follow OSOP on Facebook: https://www.facebook.com/osop.panama
>>>> >
>>>> >
>>>> > On Sat, Mar 2, 2013 at 9:28 PM, Petros Triantafyllidis <trian at auth.gr
>>>> > <mailto:trian at auth.gr>> wrote:
>>>> >
>>>> > Hello,
>>>> > I am quite new with ShakeMap and just installed it under Ubuntu
>>>> > 12.04 LTS along with GMT 4.5.7. While still in test period, I face
>>>> > problems with some of the events during plotregr, which probably
>>>> > point to ghostscript issue (GPL Ghostscript 9.05 (2012-02-08)). I
>>>> > tried both with ImageMagick/Graphicsmagick, even compiled a
>>>> > different version of ghostscript (9.07), but the result remains
>>>> > the same and pg{a,v}_regr.p{df,ng} are not produced. Although
>>>> > default event "9583161" runs smoothly I would appreciate any
>>>> > help/hint.
>>>> > Thanks in advance,
>>>> > Petros
>>>> >
>>>> >
>>>> > igctech at localhost:~/ShakeMap$ bin/shake -event auth2013cxej -verbose
>>>> > shake started at Sat Mar 2 20:49:29 2013
>>>> > 2013-03-02 20:49:29 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/retrieve -event auth2013cxej'
>>>> > 2013-03-02 20:49:30 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/pending -event auth2013cxej'
>>>> > 2013-03-02 20:49:31 : transfer: ----- Starting Transfer at
>>>> > 03/02/2013 20:49:31 -----
>>>> > 2013-03-02 20:49:31 : transfer: ----- Transfer finished at
>>>> > 03/02/2013 20:49:31 -----
>>>> > 2013-03-02 20:49:31 : shake: Done with 'pending'
>>>> > 2013-03-02 20:49:31 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/grind -event auth2013cxej -qtm
>>>> > -xml'
>>>> > 2013-03-02 20:49:36 : grind: Warning: Vs30 grid contains 6978
>>>> > invalid values. They will be replaced with the default Vs30 (686
>>>> > m/s).
>>>> > grind: Sanity check - bias_min_bias limited to -1.8
>>>> > Uncertainty computation skipped (no Intensity > 6.0)
>>>> > 2013-03-02 20:51:17 : shake: Done with 'grind'
>>>> > 2013-03-02 20:51:17 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/tag -event auth2013cxej'
>>>> > 2013-03-02 20:51:18 : shake: Done with 'tag'
>>>> > 2013-03-02 20:51:18 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/mapping -event auth2013cxej
>>>> > -timestamp -itopo'
>>>> > GMT_grd_is_global: probably, x spans exactly 360 and -90 <= y <= 90
>>>> > To make sure the grid is recognized as geographical and
>>>> > global, use the -fg option
>>>> > GMT_grd_is_global: probably, x spans exactly 360 and -90 <= y <= 90
>>>> > To make sure the grid is recognized as geographical and
>>>> > global, use the -fg option
>>>> > GMT_grd_is_global: probably, x spans exactly 360 and -90 <= y <= 90
>>>> > To make sure the grid is recognized as geographical and
>>>> > global, use the -fg option
>>>> > GMT_grd_is_global: probably, x spans exactly 360 and -90 <= y <= 90
>>>> > To make sure the grid is recognized as geographical and
>>>> > global, use the -fg option
>>>> > Printing grade - (-0.000)
>>>> > 2013-03-02 20:53:23 : shake: Done with 'mapping'
>>>> > 2013-03-02 20:53:23 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/plotregr -event auth2013cxej
>>>> > -lab_dev 6'
>>>> > 2013-03-02 20:53:24 : plotregr: ----- Starting plotregr at
>>>> > 03/02/2013 20:53:24 -----
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmoEAnGg" "--" "/tmp/gmbKkWzt" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmoEAnGg" "--" "/tmp/gmbKkWzt" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: Postscript delegate failed
>>>> > (/home/igctech/ShakeMap/bin/../data/auth2013cxej/regression/pga_regr.ps
>>>> > <http://pga_regr.ps>).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmLOQhn8" "--" "/tmp/gmCOAFoz" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmLOQhn8" "--" "/tmp/gmCOAFoz" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: Postscript delegate failed
>>>> > (/home/igctech/ShakeMap/bin/../data/auth2013cxej/regression/pga_regr.ps
>>>> > <http://pga_regr.ps>).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmgtmzfh" "--" "/tmp/gmymI0Vg" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmgtmzfh" "--" "/tmp/gmymI0Vg" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: Postscript delegate failed
>>>> > (/home/igctech/ShakeMap/bin/../data/auth2013cxej/regression/pgv_regr.ps
>>>> > <http://pgv_regr.ps>).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmPqQU14" "--" "/tmp/gmsOZ4H5" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: "gs" "-q" "-dBATCH" "-dMaxBitmap=50000000"
>>>> > "-dNOPAUSE" "-sDEVICE=pnmraw" "-dTextAlphaBits=4"
>>>> > "-dGraphicsAlphaBits=4" "-r72x72" "-g595x842"
>>>> > "-sOutputFile=/tmp/gmPqQU14" "--" "/tmp/gmsOZ4H5" "-c" "quit"
>>>> > (child process quit due to signal 9).
>>>> > /usr/bin/gm convert: Postscript delegate failed
>>>> > (/home/igctech/ShakeMap/bin/../data/auth2013cxej/regression/pgv_regr.ps
>>>> > <http://pgv_regr.ps>).
>>>> > 2013-03-02 21:45:46 : plotregr: ----- plotregr finished at
>>>> > 03/02/2013 21:45:46 -----
>>>> > 2013-03-02 21:45:47 : shake: Done with 'plotregr'
>>>> > 2013-03-02 21:45:47 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/genex -event auth2013cxej -zip
>>>> > -metadata -shape shape'
>>>> > 2013-03-02 21:46:53 : shake: Done with 'genex'
>>>> > 2013-03-02 21:46:53 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/transfer -event auth2013cxej
>>>> > -www -push'
>>>> > 2013-03-02 21:46:57 : transfer: ----- Starting Transfer at
>>>> > 03/02/2013 21:46:57 -----
>>>> > 2013-03-02 21:46:59 : transfer: ----- Transfer finished at
>>>> > 03/02/2013 21:46:59 -----
>>>> > 2013-03-02 21:46:59 : shake: Done with 'transfer'
>>>> > 2013-03-02 21:46:59 : shake: Running:
>>>> > '/home/igctech/ShakeMap/bin/../bin/setversion -event auth2013cxej'
>>>> > 2013-03-02 21:47:00 : shake: Done with 'setversion'
>>>> >
>>>> > --
>>>> > Dr. TRIANTAFYLLIDIS PETROS E-MAIL:trian at auth.gr <mailto:trian at auth.gr>
>>>> > ^^^^^^^^^^^^^^^^^^^^^^^^^^http://users.auth.gr/trian
>>>> > Aristotle University - Computer Science Department, POBox 114,
>>>> > 54124 Thessaloniki-GREECE - TEL:+30-2310998585 <tel:%2B30-2310998585>, FAX:2310998419
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Shake-dev mailing list
>>>> > Shake-dev at geohazards.usgs.gov <mailto:Shake-dev at geohazards.usgs.gov>
>>>> > https://geohazards.usgs.gov/mailman/listinfo/shake-dev
>>>> >
>>>> >
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>>>>
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>>>>
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>>>> ****************************************
>>>>
>>>>
>>
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