search

ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
374 stars 67 forks source link

Ctest failing while building with cmake #119

Open kbipinkumar opened 1 year ago

kbipinkumar commented 1 year ago

I am attempting to package FastANI on behalf of bioarchlinux project. while building using cmake with following build options i am encountering errors with ctest

# cmake -B build \
        -DCMAKE_BUILD_TYPE='None' \
        -DCMAKE_INSTALL_PREFIX='/usr' \
        -DCMAKE_SKIP_RPATH=YES \
        -Wno-dev
    cmake --build build

this is the error i am getting

# ctest --test-dir build --output-on-failure
Internal ctest changing into directory: /build/fastani/src/FastANI-1.34/build
Test project /build/fastani/src/FastANI-1.34/build
      Start  1: Single Threaded Pair Query Ref
 1/15 Test  #1: Single Threaded Pair Query Ref ................   Passed   61.51 sec
      Start  2: Single Threaded Multi Query
 2/15 Test  #2: Single Threaded Multi Query ...................***Exception: SegFault  0.09 sec
Filters: "Single Threaded Multi Query"
Randomness seeded to: 2752789222
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031001.LargeContigs.fna]
Query = [data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = stsrmq-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 0
INFO [thread 0], skch::Sketch::index, unique minimizers = 0
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (0, 0) ... 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Single Threaded Multi Query
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:74
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:74: FAILED:
due to a fatal error condition:
  SIGSEGV - Segmentation violation signal

===============================================================================
test cases: 1 | 1 failed
assertions: 1 | 1 failed

      Start  3: Single Threaded Multi Ref.
 3/15 Test  #3: Single Threaded Multi Ref. ....................***Exception: SegFault  0.08 sec
Filters: "Single Threaded Multi Ref."
Randomness seeded to: 2337037726
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Query = [data/D4/2000031001.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = stmrsq-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 0
INFO [thread 0], skch::Sketch::index, unique minimizers = 0
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (0, 0) ... 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Single Threaded Multi Ref.
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:108
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:108: FAILED:
due to a fatal error condition:
  SIGSEGV - Segmentation violation signal

===============================================================================
test cases: 1 | 1 failed
assertions: 1 | 1 failed

      Start  4: Single Threaded Multi Q. Multi Ref.
 4/15 Test  #4: Single Threaded Multi Q. Multi Ref. ...........***Exception: SegFault  0.08 sec
Filters: "Single Threaded Multi Q. Multi Ref."
Randomness seeded to: 1141743884
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031008.LargeContigs.fna, data/D4/2000031009.LargeContigs.fna]
Query = [data/D4/2000031001.LargeContigs.fna, data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = stmqmr-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 0
INFO [thread 0], skch::Sketch::index, unique minimizers = 0
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (0, 0) ... 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Single Threaded Multi Q. Multi Ref.
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:141
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:141: FAILED:
due to a fatal error condition:
  SIGSEGV - Segmentation violation signal

===============================================================================
test cases: 1 | 1 failed
assertions: 1 | 1 failed

      Start  5: Multi Threaded Multi Q. Multi Ref.
 5/15 Test  #5: Multi Threaded Multi Q. Multi Ref. ............***Exception: SegFault  0.10 sec
Filters: "Multi Threaded Multi Q. Multi Ref."
Randomness seeded to: 158809897
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031008.LargeContigs.fna, data/D4/2000031009.LargeContigs.fna]
Query = [data/D4/2000031001.LargeContigs.fna, data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 2
ANI output file = mtmqmr-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 2
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 0
INFO [thread 0], skch::Sketch::index, unique minimizers = 0
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (0, 0) ... 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Multi Threaded Multi Q. Multi Ref.
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:198
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:198: FAILED:
due to a fatal error condition:
  SIGSEGV - Segmentation violation signal

===============================================================================
test casesINFO [thread : 1], skch::main, ready to exit the loop
1 | 1 failed
assertions: 1 | 1 failed

      Start  6: Single Threaded Multi Q. Multi Ref. Repeats
 6/15 Test  #6: Single Threaded Multi Q. Multi Ref. Repeats ...***Failed   10.78 sec
Filters: "Single Threaded Multi Q. Multi Ref. Repeats"
Randomness seeded to: 315693141
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031008.LargeContigs.fna, data/D4/2000031009.LargeContigs.fna, data/repeat_64ats_2048.fa, data/repeat_128ats_2048.fa]
Query = [data/D4/2000031001.LargeContigs.fna, data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = stmqmr-rpt-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 2484960
INFO [thread 0], skch::Sketch::index, unique minimizers = 6
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (47382, 4) ... (2248048, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 10.7209 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished
ERROR :: SPLIT 0's ratio difference 682669 exceeds maximum thresholds.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Single Threaded Multi Q. Multi Ref. Repeats
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:256
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:269: FAILED:
  REQUIRE( finalResults.size() == 6 )
with expansion:
  0 == 6

===============================================================================
test cases: 1 | 1 failed
assertions: 1 | 1 failed

      Start  7: Multi Threaded Multi Q. Multi Ref. Repeats
 7/15 Test  #7: Multi Threaded Multi Q. Multi Ref. Repeats ....***Failed    6.97 sec
Filters: "Multi Threaded Multi Q. Multi Ref. Repeats"
Randomness seeded to: 3551805892
>>>>>>>>>>>>>>>>>>
Reference = [data/D4/2000031008.LargeContigs.fna, data/D4/2000031009.LargeContigs.fna, data/repeat_64ats_2048.fa, data/repeat_128ats_2048.fa]
Query = [data/D4/2000031001.LargeContigs.fna, data/D4/2000031004.LargeContigs.fna, data/D4/2000031006.LargeContigs.fna]
Kmer size = 16
Fragment length = 3000
Threads = 2
ANI output file = mtmqmr-rpt-test.txt
Sanity Check  = 1
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 2
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 976744
INFO [thread 0], skch::Sketch::index, unique minimizers = 6
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (31507, 4) ... (819208, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 6.45124 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO [thread 1], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished
ERROR :: SPLIT 0's ratio difference 341335 exceeds maximum thresholds.
ERROR :: SPLIT 1's ratio difference 341333 exceeds maximum thresholds.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fastANITest is a Catch2 v3.4.0 host application.
Run with -? for options

-------------------------------------------------------------------------------
Multi Threaded Multi Q. Multi Ref. Repeats
-------------------------------------------------------------------------------
/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:278
...............................................................................

/build/fastani/src/FastANI-1.34/tests/fastani_tests.cpp:291: FAILED:
  REQUIRE( finalResults.size() == 6 )
with expansion:
  0 == 6

===============================================================================
test cases: 1 | 1 failed
assertions: 1 | 1 failed

      Start  8: Repeat A2048 and 8AT
 8/15 Test  #8: Repeat A2048 and 8AT ..........................   Passed    4.62 sec
      Start  9: Repeat A2048 and 12AT
 9/15 Test  #9: Repeat A2048 and 12AT .........................   Passed    4.46 sec
      Start 10: Repeat A2048 and 16AT
10/15 Test #10: Repeat A2048 and 16AT .........................   Passed    4.59 sec
      Start 11: Repeat A2048 and 20AT
11/15 Test #11: Repeat A2048 and 20AT .........................   Passed    4.46 sec
      Start 12: Repeat A2048 and 24AT
12/15 Test #12: Repeat A2048 and 24AT .........................   Passed    4.67 sec
      Start 13: Repeat A2048 and 32AT
13/15 Test #13: Repeat A2048 and 32AT .........................   Passed    4.59 sec
      Start 14: Repeat A2048 and 64AT
14/15 Test #14: Repeat A2048 and 64AT .........................   Passed    5.25 sec
      Start 15: Repeat A2048 and 128AT
15/15 Test #15: Repeat A2048 and 128AT ........................   Passed    5.73 sec

60% tests passed, 6 tests failed out of 15

Total Test time (real) = 118.00 sec

The following tests FAILED:
      2 - Single Threaded Multi Query (SEGFAULT)
      3 - Single Threaded Multi Ref. (SEGFAULT)
      4 - Single Threaded Multi Q. Multi Ref. (SEGFAULT)
      5 - Multi Threaded Multi Q. Multi Ref. (SEGFAULT)
      6 - Single Threaded Multi Q. Multi Ref. Repeats (Failed)
      7 - Multi Threaded Multi Q. Multi Ref. Repeats (Failed)
Errors while running CTest

could anyone give pointers regarding whats going wrong?

srirampc commented 1 year ago

I am not sure what the issue is. You can try with -DCMAKE_BUILD_TYPE=Debug and see if it can provide little more detail.

It it doesn't work, you can skip tests for now by adding the option -DBUILD_TESTING=OFF.