GMT 5 much slower than GMT 4? #587

alomax · 2019-03-29T08:33:16Z

Equivalent command line scripts take more than twice as long to run in GMT 5 than in GMT 4

We use GMT extensively for maps, earthquake mechanisms and other plots in a time-sensitive, real-time system: http://early-est.alomax.net

The latest versions of our software using GMT 5 are broken because the plotting and reporting module does not complete fast enough. We suspect this may be primarily due to much the longer processing time needed for command line GMT 5 than for GMT 4:

~/temp> gmt --version
GMT Version 4.5.7
~/temp> time ./test_GMT4.bash 
real	0m0.212s
user	0m0.146s
sys	0m0.050s
~/temp> time ./test_GMT4.bash 
real	0m0.194s
user	0m0.136s
sys	0m0.043s
~/temp> time ./test_GMT4.bash 
real	0m0.244s
user	0m0.139s
sys	0m0.044s
~/temp> time ./test_GMT4.bash 
real	0m0.190s
user	0m0.132s
sys	0m0.043s

~/temp> gmt --version
5.4.5
~/temp> time test_GMT5.bash 
real	0m0.455s
user	0m0.597s
sys	0m0.450s
~/temp> time test_GMT5.bash 
real	0m0.477s
user	0m0.530s
sys	0m0.500s
~/temp> time test_GMT5.bash 
real	0m0.415s
user	0m0.703s
sys	0m0.366s
~/temp> time test_GMT5.bash 
real	0m0.420s
user	0m0.643s
sys	0m0.404s

Full scripts that show the difference in run time:

https://www.dropbox.com/s/0asx13o1ahiz1dr/test_GMT4.bash?dl=0
https://www.dropbox.com/s/cz0acpj4cueyatz/test_GMT5.bash?dl=0

System information

Operating system:
System Version: OS X 10.10.5 (14F2511)
Kernel Version: Darwin 14.5.0
Hardware:
Model Name: iMac
Model Identifier: iMac14,2
Processor Name: Intel Core i7
Processor Speed: 3.5 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Memory: 16 GB
Version of GMT: 4.5.7 and 5.4.5

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welcome · 2019-03-29T08:33:19Z

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PaulWessel · 2019-03-29T18:46:31Z

Hi @alomax, you are right that GMT5 is slower than GMT4 for many tasks, especially table i/o. The key reason for this is that the entire i/o machinery was replaced to enable us to extend GMT to other platforms such as MATLAB, Python, Julia and more via the API. As such, the API is a bit immature and has room for optimizing. It would be helpful to see your actual scripts for the jobs that are timing out as we may be able to offer some advice for the short-term, and hopefully we can also determine which are the most critical bottlenecks. For instance, if you have fixed areas and you are running pscoast, consider running that once, store the PostScript overlay, and simply cat it in place as needed instead of re-running the same command, etc.

joa-quim · 2019-03-29T22:55:00Z

But it's nevertheless strange that the script is made up of basically pscoast calls (+ psscale). why would this be slower?

PaulWessel · 2019-03-29T22:59:03Z

Yes, those are both unaffected by the i/o changes so perhaps we need to run a time and eventually profiling of the calls.

anbj · 2019-03-30T06:58:20Z

Not really comparable, but maybe a relevant footnote; http://gmt.soest.hawaii.edu/boards/1/topics/7996.

alomax · 2019-04-01T08:05:53Z

Thanks for the extensive comments @PaulWessel, and also @joa-quim and @abanbj

Here are the scripts, but the ensemble is a monster! https://www.dropbox.com/s/8gsszu86ts4k9m9/EarlyEest_GMT5_scripts.tgz?dl=0

We do have a fixed, world map, but for each earthquake detected there is a regional map with center at the current earthquake epicenter.

Is perhaps the main increase in execution time GMT5 vs GMT4 due to the creation and management of a new session GMT_Create_Session() for each gmt command called from the command line in a script?
If so, is the absolute, most efficient way to run GMT5+ to use a single, compiled C driver program which calls all gmt "commands" as module functions through the C API?

Thanks,
Anthony

joa-quim · 2019-04-01T11:24:12Z

Don't think the GMT_Create_Session() is to blame here. I made a quick benchmark in Julia. Just created functions with GMT_Create_Session() and destroy.

function sess1()
	API = GMT.GMT_Create_Session("GMT", 2, GMT.GMT_SESSION_NOEXIT + GMT.GMT_SESSION_EXTERNAL + GMT.GMT_SESSION_COLMAJOR)
end


function sess2()
	API = GMT.GMT_Create_Session("GMT", 2, GMT.GMT_SESSION_NOEXIT + GMT.GMT_SESSION_EXTERNAL + GMT.GMT_SESSION_COLMAJOR)
	gmt("destroy") 
end

and timings are

julia> @btime sess2()
  23.003 ms (11 allocations: 416 bytes)

julia> @btime sess1()
  10.613 ms (0 allocations: 0 bytes)

So, actually, destroy takes a little longer than create. And these tests were done with a GMT debug build (if that even matter for these tests).

Ah, and remind that these timings include the Julia parsing too, though they presumably very small.

alomax · 2019-04-01T12:42:49Z

@joa-quim I was wondering if the whole session architecture and management overhead is the main difference GMT 5 vs GMT 4 when run as individual commands from the shell. Not just the initial GMT_Create_Session() call.

joa-quim · 2019-04-01T12:54:27Z

Yes, not impossible, but in that case a single, tailored, executable with all the commands for your needs wouldn't be substantially faster since it would use the same architecture anyway.

alomax · 2019-04-01T13:02:50Z

But in GMT 5 it looks like each call to gmt <module> through the command line sets up a new session (and presumably manages it and cleans up / destroys later), and then calls the module function.
line 93-: https://github.com/GenericMappingTools/gmt/blob/master/src/gmt.c

While doing all in a single program with the new API would only set up one session.

joa-quim · 2019-04-01T13:29:11Z

Yes, and that is why I tested the timings for creating and deleting new sessions. Aside from the time consumed in in creating/deleting new sessions, both the single exe and the multiple commands solutions should spend the same time in managing the sessions. Off course I may be wrong and nothing like testing.

BTW, maintaining a single session is what the Julia wrapper does for the GMT scripts, but one has to pay also the parsing time plus some memory copies that sometimes must be made.

joa-quim · 2019-04-01T15:37:07Z

A bit intriguing. psscale -Z is way slower that discrete.

disc = makecpt("-Crainbow -T-20/60/10");
cont = makecpt("-Crainbow -T-20/60/10 -Z");

tic()
psscale(D="x1i/5i+w4i/0.5i+h", B="+tdiscrete", I=0.5, C=disc)
toc()
tic()
psscale(D="x1i/7i+w4i/0.5i+h", B="+tcontinuous", I=0.5, C=cont)
toc()

timings vary a bit but the relation is close to this

elapsed time: 0.003415336 seconds
elapsed time: 0.152392377 seconds

alomax · 2019-04-02T15:45:18Z

But in GMT 5 it looks like each call to gmt <module> through the command line sets up a new session (and presumably manages it and cleans up / destroys later), and then calls the module function.
line 93-: https://github.com/GenericMappingTools/gmt/blob/master/src/gmt.c

While doing all in a single program with the new API would only set up one session.

PaulWessel · 2019-04-03T03:32:02Z

I would think the i/o is where the slowness is but we will need to have a look. If you scripts do a bunch of GMT calls building a plot then it would be possible to write a C program that just called Create, a bunch of GMT_Call_Module with strings, and GMT_Destroy. So you would save all those Create/Destroy times which certainly takes some time. But I don't want to send you down that path with the promise of speedup without doing some more testing.

alomax · 2019-04-03T07:58:42Z

Yes, it may be that a combination of i/o and Create/Destroy in many gmt calls is a major cause of slowness. In our scripts, there is a set of many psxy calls which shows up in timing tests as a relatively large user of time:

# plot requested and active background colors
gmt psxy ${PLOT_DATA_PATH}/sta.requested.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL[0]} -W0.2,0/0/0 -G${STA_REQUESTED_COLOR}  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/sta.healthy.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL[0]} -W0.2,0/0/0 -G${STA_ACTIVE_COLOR}  -O -K >> ${PS_NAME}
# plot available warning levels - t50
gmt psxy ${PLOT_DATA_PATH}/t50.sta.ltgreen.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G127/191/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/t50.sta.ltyellow.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G191/191/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/t50.sta.ltred.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G191/127/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/t50.sta.green.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G0/255/0  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/t50.sta.yellow.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G255/255/0  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/t50.sta.red.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_LOWER_RIGHT} -G255/0/0  -O -K >> ${PS_NAME}
# plot available warning levels - t50
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.ltgreen.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G127/191/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.ltyellow.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G191/191/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.ltred.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G191/127/127  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.green.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G0/255/0  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.yellow.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G255/255/0  -O -K >> ${PS_NAME}
gmt psxy ${PLOT_DATA_PATH}/tauc.sta.red.xy ${R_VAL} ${J_VAL} -: ${N_VAL} ${SYMBOL_UPPER_LEFT} -G255/0/0  -O -K >> ${PS_NAME}

It does seem likely that an envelope C program instead of bash script would be (much) more efficient. But I will wait for more testing proof. And we do not currently have €€€€ for such development (€) and testing (€€€) of new envelope C programs...

stale · 2019-07-02T08:50:34Z

This issue has been automatically marked as stale because it has not had activity in the last 90 days. It will be closed if no further activity occurs within 7 days. Thank you for your contributions.

stale · 2019-10-01T16:04:36Z

This issue has been automatically marked as stale because it has not had activity in the last 90 days. It will be closed if no further activity occurs within 7 days. Thank you for your contributions.

seisman · 2019-10-02T17:39:55Z

It seems there is nothing we can do here. Closing?

PaulWessel · 2019-10-02T17:50:29Z

No, simply have not had time to investigate - lets keep it alive.

joa-quim mentioned this issue May 9, 2019

Specify file names that cause errors without having to specify verbose output #692

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stale bot added the stale This will not be worked on label Jul 2, 2019

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PaulWessel added the longterm Long standing issues that need to be resolved label Oct 2, 2019

alomax mentioned this issue Jan 17, 2022

Grid2GMT: upgrade supported GMT version and change to bash script? ut-beg-texnet/NonLinLoc#15

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sean0921 mentioned this issue Aug 23, 2022

Grid2GMT: upgrade supported GMT version and change to bash script ut-beg-texnet/NonLinLoc#30

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GMT 5 much slower than GMT 4? #587

GMT 5 much slower than GMT 4? #587

alomax commented Mar 29, 2019

welcome bot commented Mar 29, 2019

PaulWessel commented Mar 29, 2019

joa-quim commented Mar 29, 2019

PaulWessel commented Mar 29, 2019

anbj commented Mar 30, 2019

alomax commented Apr 1, 2019

joa-quim commented Apr 1, 2019 •

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alomax commented Apr 1, 2019

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PaulWessel commented Apr 3, 2019

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stale bot commented Jul 2, 2019

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seisman commented Oct 2, 2019

PaulWessel commented Oct 2, 2019

GMT 5 much slower than GMT 4? #587

GMT 5 much slower than GMT 4? #587

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alomax commented Mar 29, 2019

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PaulWessel commented Mar 29, 2019

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