[Shake-dev] Postscript delegate failed
Petros Triantafyllidis
trian at auth.gr
Wed Nov 20 15:30:17 UTC 2013
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 <http://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
> <mailto:trian at auth.gr>> wrote:
>
> Dear Billy,
> My mistake: You have to remove "-O2" CFLAG from config.mk
> <http://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).
> <mailto:shake-dev%40geohazards.usgs.gov?Subject=Re%3A%20%5BShake-dev%5D%20Errors%20with%20grind&In-Reply-To=%3C4F6B9342.2080901%40cicese.mx%3E>
> 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> <mailto:trian at auth.gr>
>> *Para:* Billy edson Burgoa Rosso <billyburgoa at yahoo.com>
>> <mailto:billyburgoa at yahoo.com>
>> *CC:* shake-dev at geohazards.usgs.gov
>> <mailto: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
>> <http://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 <mailto:trian at auth.gr>>
>>> To: Branden Christensen <branden.christensen at osop.com.pa
>>> <mailto:branden.christensen at osop.com.pa>>
>>> Cc: shake-dev at geohazards.usgs.gov
>>> <mailto:shake-dev at geohazards.usgs.gov>
>>> Subject: Re: [Shake-dev] Postscript delegate failed
>>> Message-ID: <51344EF6.7040104 at auth.gr
>>> <mailto: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>
>>> <mailto:branden.christensen at osop.com.pa
>>> <mailto:branden.christensen at osop.com.pa>>*
>>> > www.osop.com.pa <http://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>
>>> > <mailto: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>
>>> > <http://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>
>>> > <http://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>
>>> > <http://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>
>>> > <http://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> <mailto: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> <tel:%2B30-2310998585>, FAX:2310998419
>>> >
>>> >
>>> > _______________________________________________
>>> > Shake-dev mailing list
>>> > Shake-dev at geohazards.usgs.gov
>>> <mailto:Shake-dev at geohazards.usgs.gov>
>>> <mailto: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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