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A read-only Git copy of the OpenBenchmarking.org test profiles.
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Windows: pts/mafft-1.6.1 fails to produce result for most runs #170

Open mirror176 opened 4 years ago

mirror176 commented 4 years ago

batch-benchmark fails all but the first test, debug-benchmark always succeeds and debug-result-parser always fails to produce a result. Not sure how to get further with debugging run when debug-benchmark always succeeds but does mention environment variable issue. Sample output below:

.\phoronix-test-suite batch-benchmark mafft

Starting the Phoronix Test Suite

     Evaluating External Test Dependencies ..........................................................................

Phoronix Test Suite v10.0.0m1

Installed:     pts/mafft-1.6.1

System Information

PROCESSOR: Intel Core i7-3820 @ 3.60GHz Core Count: 4 Thread Count: 8 Cache Size: 256 MB Core Family: Sandy Bridge

GRAPHICS: NVIDIA GeForce GTX 660 2GB Display Driver: 456.38 (27.21.14.5638) Screen: 1920x1080

MOTHERBOARD: ASUS SABERTOOTH X79 BIOS Version: 4801 Network: AnchorFree TAP-Windows V9 + VirtualBox Host-Only

MEMORY: 4 x 8192 MB 1333MHz F3-12800CL10-8GBZ

DISK: 1863GB WDC WD2003FZEX-00Z4SA0

Timed MAFFT Alignment 7.471: pts/mafft-1.6.1 Test 1 of 1 Estimated Trial Run Count: 3 Estimated Time To Completion: 1 Minute [11:15 MDT] Started Run 1 @ 11:14:50 Started Run 2 @ 11:15:01 The test run did not produce a result. Started Run 3 @ 11:15:06 The test run did not produce a result. Started Run 4 @ 11:15:10 The test run did not produce a result. Started Run 5 @ 11:15:15 The test run did not produce a result.

Multiple Sequence Alignment - LSU RNA:
    6.57

Average: 6.57 Seconds
Samples: 1

Results Uploaded To: https://openbenchmarking.org/result/2009303-FI-20200930165

.\phoronix-test-suite debug-result-parser mafft Starting the Phoronix Test Suite

======================================== Phoronix Test Suite v10.0.0m1 System Information

PROCESSOR: Intel Core i7-3820 @ 3.60GHz Core Count: 4 Thread Count: 8 Cache Size: 256 MB Core Family: Sandy Bridge

GRAPHICS: NVIDIA GeForce GTX 660 2GB Display Driver: 456.38 (27.21.14.5638) Screen: 1920x1080

MOTHERBOARD: ASUS SABERTOOTH X79 BIOS Version: 4801 Network: AnchorFree TAP-Windows V9 + VirtualBox Host-Only

MEMORY: 4 x 8192 MB 1333MHz F3-12800CL10-8GBZ

DISK: 1863GB WDC WD2003FZEX-00Z4SA0

Log File: C:\Users\Bomarc.phoronix-test-suite\installed-tests\pts\mafft-1.6.1\mafft-1.6.1-1601485483-1.log

The test run did not produce a result.

Log File At: C:\Users\Bomarc.phoronix-test-suite\installed-tests\pts\mafft-1.6.1\mafft-1.6.1-1601485483-1.log

The following tests failed to properly run:

- pts/mafft-1.6.1

.\phoronix-test-suite debug-benchmark mafft Starting the Phoronix Test Suite

     Evaluating External Test Dependencies ..........................................................................

Phoronix Test Suite v10.0.0m1

Installed:     pts/mafft-1.6.1

======================================== Phoronix Test Suite v10.0.0m1 System Information

PROCESSOR: Intel Core i7-3820 @ 3.60GHz Core Count: 4 Thread Count: 8 Cache Size: 256 MB Core Family: Sandy Bridge

GRAPHICS: NVIDIA GeForce GTX 660 2GB Display Driver: 456.38 (27.21.14.5638) Screen: 1920x1080

MOTHERBOARD: ASUS SABERTOOTH X79 BIOS Version: 4801 Network: AnchorFree TAP-Windows V9 + VirtualBox Host-Only

MEMORY: 4 x 8192 MB 1333MHz F3-12800CL10-8GBZ

DISK: 1863GB WDC WD2003FZEX-00Z4SA0

======================================== Timed MAFFT Alignment (Run 1 of 1)

Test Run Command: cd C:\Users\Bomarc.phoronix-test-suite\installed-tests\pts/mafft-1.6.1\ && ./mafft 2>&1

Test Result Montioring Process Returning: 6.633

It may take a while before the calculation starts if being scanned by anti-virus software. Also consider using a faster version for Windows 10: https://mafft.cbrc.jp/alignment/software/wsl.html

v0.000 != v7.471 (2020/Jul/3)

There is a problem in the configuration of your shell. Check the MAFFT_BINARIES environmental variable by $ echo $MAFFT_BINARIES

This variable must be unset, unless you have installed MAFFT with a special configuration. To unset this variable, type $ unset MAFFT_BINARIES or % unsetenv MAFFT_BINARIES Then retry $ mafft input > output

To keep this change permanently, edit setting files (.bash_profile, .profile, .cshrc, etc) in your home directory to delete the MAFFT_BINARIES line. On MacOSX, also edit or remove the .MacOSX/environment.plist file and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7).

Please send a problem report to katoh@ifrec.osaka-u.ac.jp, if this problem remains.

Log File At: C:\Users\Bomarc.phoronix-test-suite\installed-tests\pts\mafft-1.6.1\mafft-1.6.1-1601486469-1.log

######################################## Timed MAFFT Alignment: Multiple Sequence Alignment - LSU RNA

6.633 Seconds

Average: 6.633 Seconds ########################################

Result compared to 76 OpenBenchmarking.org samples since 26 September; median result: 12.28. Box plot of samples:
[      |-----------------------*--------------------------------------------------------------------------*#*!*|*  ]
                                                                                             This Result: 6.633 ^
                               ^ Intel Core i7-6700HQ: 160                          2 x AMD EPYC 7742: 10.654 ^
                                                                                Intel Core i7-8565U: 14.714 ^
                                                                            Intel Xeon E5-2609 v4: 19.557 ^
michaellarabel commented 4 years ago

debug-result-parser failing in this case would be expected as it's a timed test, should probably add a note about that to PTS. So far though I am unable to reproduce this issue of MAFFT sometimes failing on my Linux or Windows systems. It is most likely a problem with upstream MAFFT software itself that it ends up failing sometimes when running on Windows as the only explanation that I see at this point.