Wrapping SmartCyp

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Message 2756 - Posted: 21 Feb 2013, 7:33:58 UTC
Last modified: 21 Feb 2013, 7:58:27 UTC

So today is my 'stay-at-home' day, the one free day I may have this week before my mother takes up all my attention again. See, the personal thing I posted about in the news thread was that my mother got her third CVA last week, in the middle of local carnaval (Mardi Gras), with our doctor celebrating that festivity.

I just threw everything from my agenda and went to care for her, until I found professional help to take over from me. But even with that now found, my mother still calls on me every day. She'll probably telephone me later, but she knows I am not coming today. :-)

So... I think I have time to work further on wrapping SmartCyp.

OK, so far I have found that the executable that I built does work, when run stand-alone. Although it throws some Java errors, but seeing how with the short task the output isn't in any way affected, I doubt this is much of a problem.

No, the problem is file sizes and amount of memory that they take up.

The short task that I test with is roughly 14KB in size and runs for 233 iterations, which take, including writing the output files, about 30 seconds.
So the input file is 14 KB, the output file is however 221KB for the .CVS file and 5,114KB for the .HTML file. Its memory use is approximately 200MB, doable on your computers.

However, the larger files that Andrey wants to use as well are...
192MB when zipped, yet between 600 and 770MB when unzipped. I haven't found out yet how long they run for, but max memory use I found thus far is 1,070,232KB per task.

So either we run short tasks with large output, or we run large tasks with unknown (but expected extremely large) output. In both cases I'll hear you scream at me. ;-)

... this is going to take a lot of head scratching.
Jord

'Cause you seem like an orchard of mines, Just take one step at a time.
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Message 2757 - Posted: 21 Feb 2013, 7:37:10 UTC - in response to Message 2756.  

Although it throws some Java errors, but seeing how with the short task the output isn't in any way affected, I doubt this is much of a problem.

For the Javists out there...

 ************** Processing SMARTS and Energies **************

 ************** Reading molecule structures **************
File ‼filter not found
java.io.FileNotFoundException: ‼filter (The filename, directory name, or volume label syntax is incorrect)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)
File 40 not found
java.io.FileNotFoundException: 40 (The system cannot find the file specified) 
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)
File ‼nocsv not found
java.io.FileNotFoundException: ‼nocsv (The filename, directory name, or volume label syntax is incorrect)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)
File ‼nohtml not found
java.io.FileNotFoundException: ‼nohtml (The filename, directory name, or volume label syntax is incorrect)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)
File ‼outputfile not found
java.io.FileNotFoundException: ‼outputfile (The filename, directory name, or volume label syntax is incorrect)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)
File approved_out not found
java.io.FileNotFoundException: approved_out (The system cannot find the file specified)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(Unknown Source)
        at java.io.FileReader.<init>(Unknown Source)
        at smartcyp.SMARTCyp.readInStructures(SMARTCyp.java:389)
        at smartcyp.SMARTCyp.main(SMARTCyp.java:199)

Jord

'Cause you seem like an orchard of mines, Just take one step at a time.
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Message 2758 - Posted: 21 Feb 2013, 8:03:41 UTC

OK, so the 550MB tasks don't have any molecules in them, while the 755MB task I just ran runs out of memory. Sigh. Recompiling. :)
Jord

'Cause you seem like an orchard of mines, Just take one step at a time.
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Message 2759 - Posted: 21 Feb 2013, 8:17:41 UTC - in response to Message 2758.  

Well, 1024MB was the maximum I had given it earlier.
In the mean time I tested with 4GB, 3, even 2, but 1.5Gb is the maximum that it wants to take to allow any work to begin. I only just noticed that the output file isn't being generated, so more stuff to figure out. :)
Jord

'Cause you seem like an orchard of mines, Just take one step at a time.
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