Open mirror176 opened 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.
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
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
14902GB Seagate Expansion Desk USB File-System: NTFS
OPERATING SYSTEM: Microsoft Windows 10 Pro Build 19041 Kernel: 10.0 (x86_64) Compiler: GCC 8.1.0 + Clang 10.0.0 Security: __user pointer sanitization: Disabled
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.
.\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
14902GB Seagate Expansion Desk USB File-System: NTFS
OPERATING SYSTEM: Microsoft Windows 10 Pro Build 19041 Kernel: 10.0 (x86_64) Compiler: GCC 8.1.0 + Clang 10.0.0 Security: __user pointer sanitization: Disabled
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:
.\phoronix-test-suite debug-benchmark mafft Starting the Phoronix Test Suite
Phoronix Test Suite v10.0.0m1
======================================== 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
14902GB Seagate Expansion Desk USB File-System: NTFS
OPERATING SYSTEM: Microsoft Windows 10 Pro Build 19041 Kernel: 10.0 (x86_64) Compiler: GCC 8.1.0 + Clang 10.0.0 Security: __user pointer sanitization: Disabled
======================================== 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 ########################################