[AMBER] NetCDF error: Invalid argument

From: xu qingliang <xuqingliangouc.hotmail.com>
Date: Mon, 22 May 2017 06:28:03 +0000

Dear David,

Thanks for your reply ! We have tried different strategies based on your suggestions.

>>>Does the error depend in any way on the specifics of the system you are
running? Do the test cases run correctly on the national laboratory computer?>>>>>>

No, there is no dependent on the systems. We have tried different systems. We have run all these systems in the machine of our own lab, and everything are working well. It seems to our system has run on the machine of the national lab. There is log file, but not the trajectory file or coordinate file. I have checked the log.out file, and I could find an error at the end. But I cannot understand.

                    FINAL RESULTS

   5000 -5.1597E+05 1.1946E-01 1.1326E+01 Na+ 59780

 BOND = 35711.6354 ANGLE = 7251.0023 DIHED = 32097.0014
 VDWAALS = 61854.2916 EEL = -746301.8514 HBOND = 0.0000
 1-4 VDW = 9500.0869 1-4 EEL = 83916.7562 RESTRAINT = 0.0000
NetCDF error: Invalid argument

>>>>Can you run your test case in serial mode? I note that you are using 240
threads for you calculation--this is both likley to be very inefficient,
and may trigger errors that we don't test for very much. So try a short
parallel simulation with a much smaller number of threads.>>>>>

Yes, we have tried on one cpu wtih 24 cores, but the problem is the same.

Thanks for your help again !

Best wishes,

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Received on Sun May 21 2017 - 23:30:03 PDT
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