# PETSc Testing System¶

The PETSc test system consists of

• A language contained within the example source files that describes the tests to be run

• The test generator (config/gmakegentest.py) that at the make step parses the example source files and generates the makefiles and shell scripts.

• The petsc test harness that consists of makefile and shell scripts that runs the executables with several logging and reporting features.

Details on using the harness may be found in the PETSc Users Manual.

In the examples below, we often make use of this command: make -f gmakefile ... or when testing, we have the equivalent of make -f gmakefile.test .... Here is a useful alias:

alias ptmake='make -f gmakefile.test'


where ptmake stands for “petsc test make”. We will use this syntax below to make the commands nicer.

## Determining the failed jobs of a given run¶

The running of the test harness will show which tests fail, but you may not have logged the output or run without showing the full error. The best way of examining the errors is with this command:

$EDITOR$PETSC_ARCH/tests/test*err.log


This method can also be used for pipeline jobs. Failed jobs can have all of the log files downloaded from the artifacts download tab on the right side:

To see the list of all tests that failed from the last run, you can also run this command:

ptmake print-test test-fail=1


To print it out in a column format:

ptmake print-test test-fail=1 | tr ' ' '\n' | sort


Once you know which tests failed, the question is how to debug them.

## Introduction to debugging workflows¶

Here, two different workflows on developing with the test harness are presented, and then the language for adding a new test is described. Before describing the workflow, we first discuss the output of the test harness and how it maps onto makefile targets and shell scripts.

Consider this line from running the PETSc test system:

TEST arch-ci-linux-uni-pkgs/tests/counts/vec_is_sf_tests-ex1_basic_1.counts


The string vec_is_sf_tests-ex1_basic_1 gives the following information:

• The file generating the tests is found in $PETSC_DIR/src/vec/is/sf/tests/ex1.c • The makefile target for the test is vec_is_sf_tests-ex1_basic_1 • The makefile target for the executable is$PETSC_ARCH/tests/vec/is/sf/tests/ex1

• The shell script running the test is located at: $PETSC_DIR/$PETSC_ARCH/tests/vec/is/sf/tests/runex1_basic_1.sh

Let’s say that you want to debug a single test as part of development. There are two basic methods of doing this: 1) use shell script directly in test directory, or 2) use makefile from the top level directory. We present both workflows. There are many permutations of this and a developer should always find the method that makes them the most productive.

## Debugging a PETSc test using shell scripts¶

First, suggest looking at the working directory and look at the options to the scripts:

> cd $PETSC_ARCH/tests/vec/is/sf/tests > ./runex1_basic_1.sh -h Usage: ./runex1_basic_1.sh [options] OPTIONS -a <args> ......... Override default arguments -c ................ Cleanup (remove generated files) -C ................ Compile -d ................ Launch in debugger -e <args> ......... Add extra arguments to default -f ................ force attempt to run test that would otherwise be skipped -h ................ help: print this message -n <integer> ...... Override the number of processors to use -j ................ Pass -j to petscdiff (just use diff) -J <arg> .......... Pass -J to petscdiff (just use diff with arg) -m ................ Update results using petscdiff -M ................ Update alt files using petscdiff -o <arg> .......... Output format: 'interactive', 'err_only' -p ................ Print command: Print first command and exit -t ................ Override the default timeout (default=60 sec) -U ................ run cUda-memcheck -V ................ run Valgrind -v ................ Verbose: Print commands  We will be using the -C, -V, and -p flags. A basic workflow is something similar to: <edit> runex1_basic_1.sh -C <edit> ... runex1_basic_1.sh -m # If need to update results ... runex1_basic_1.sh -V # Make sure valgrind clean cd$PETSC_DIR
git commit -a


For loops sometimes can become onerous to run the whole test. In this case, you can use the -p flag to print just the first command. It will print a command suitable for running from $PETSC_DIR, but it is easy to modify for execution in the test directory: runex1_basic_1.sh -p  ## Debugging a single PETSc test using makefile¶ First recall how to find help for the options: ptmake help-test  To compile the test and run it: ptmake test search=vec_is_sf_tests-ex1_basic_1  This can consist of your basic workflow. However, for the normal compile and edit, running the entire harness with search can be cumbersome. So first get the command: ptmake vec_is_sf_tests-ex1_basic_1 PRINTONLY=1 <copy command> <edit> ptmake$PETSC_ARCH/tests/vec/is/sf/tests/ex1
/scratch/kruger/contrib/petsc-mpich-cxx/bin/mpiexec -n 1 arch-mpich-cxx-py3/tests/vec/is/sf/tests/ex1
...
cd $PETSC_DIR git commit -a  ## Advanced searching¶ For forming a search, it is recommended to always use print-test instead of test to make sure it is returning the values that you want. The three basic and recommended arguments are: • search (or s) • Searches based on name of test target (see above) • Use the familiar glob syntax (like the Unix ls command) • Example: ptmake print-test search='vec_is*ex1*basic*1' • Equivalently: ptmake print-test s='vec_is*ex1*basic*1' • It also takes full paths • Example: ptmake print-test s='src/vec/is/tests/ex1.c' • Example: ptmake print-test s='src/dm/impls/plex/tests/' • Example: ptmake print-test s='src/dm/impls/plex/tests/ex1.c' • query and queryval (or q and qv) • query corresponds to test harness keyword, queryval to the value. • Example: ptmake print-test query='suffix' queryval='basic_1' • Invokes config/query_tests.py to query the tests (see config/query_tests.py --help for more information). • See below for how to use as it has many features • searchin (or i) • Filters results of above searches • Example: ptmake print-test s='src/dm/impls/plex/tests/ex1.c' i='*refine_overlap_2d*' Searching using gmake’s native regexp functionality is kept for people who like it, but most developers will likely prefer the above methods: • gmakesearch • Use gmake’s own filter capability. • Fast, but requires knowing gmake regex syntax which uses % instead of * • Also very limited (cannot use two %’s for example) • Example: ptmake test gmakesearch='vec_is%ex1_basic_1' • gmakesearchin • Use gmake’s own filter capability to search in previous results • Example: ptmake test gmakesearch='vec_is%1' gmakesearchin='basic' • argsearch • search on arguments using gmake. This is deprecated in favor of the query/queryval method as described below. • Example: ptmake test argsearch='sf_type' • Not very powerful ### Query-based searching¶ Basic examples. Note the the use of glob style matching is also accepted in the value field: • Example: ptmake print-test query='suffix' queryval='basic_1' • Example: ptmake print-test query='requires' queryval='cuda' • Example: ptmake print-test query='requires' queryval='define(PETSC_HAVE_MPI_GPU_AWARE)' • Example: ptmake print-test query='requires' queryval='*GPU_AWARE*' Using the name field is equivalent to the search above: • Example: ptmake print-test query='name' queryval='vec_is*ex1*basic*1' • Useful because this can be combined with union/intersect queries as discussed below Arguments are tricky to search for. Consider: args: -ksp_monitor_short -pc_type ml -ksp_max_it 3  Search terms are: ksp_monitor, 'pc_type ml', ksp_max_it  Certain items are ignored: • Numbers (see ksp_max_it above), but floats are ignored as well. • Loops: args: -pc_fieldsplit_diag_use_amat {{0 1}} gives pc_fieldsplit_diag_use_amat as the search term • Input files: -f * Examples of argument searching: • ptmake print-test query='args' queryval='ksp_monitor' • ptmake print-test query='args' queryval='*monitor*' • ptmake print-test query='args' queryval='pc_type ml' Multiple simultaneous queries can be performed with union (,), and intesection (|) operators in the query field. Examples: • ptmake print-test query='requires,requires' queryval='cuda,hip' • All examples using cuda + all examples using hip • ptmake print-test query='requires|requires' queryval='ctetgen,triangle' • Examples that require both triangle and ctetgen (intersection of tests) • ptmake print-test query='requires,requires' queryval='ctetgen,triangle' • Tests that require either ctetgen or triangle • ptmake print-test query='requires|name' queryval='cuda,dm*' • Find cuda examples in the dm package. Here is a way of getting a feel for how the union and intersect operators work: > ptmake print-test query='requires' queryval='ctetgen' | tr ' ' '\n' | wc -l 170 > ptmake print-test query='requires' queryval='triangle' | tr ' ' '\n' | wc -l 330 > ptmake print-test query='requires,requires' queryval='ctetgen,triangle' | tr ' ' '\n' | wc -l 478 > ptmake print-test query='requires|requires' queryval='ctetgen,triangle' | tr ' ' '\n' | wc -l 22  The total number of tests for running only ctetgen or triangle is 500. They have 22 tests in common, and 478 that run independently of each other. • The union and intersection have fixed grouping. So this string argument: query='requires,requires|args' queryval='cuda,hip,*log*'  will can be read as: requires:cuda && (requires:hip || args:*log*)  which is probably not what is intended. query/queryval also support negation (!), but is limited. The negation only applies to tests that have a related field in it. So for example, the arguments of: query=requires queryval='!cuda'  will only match if they explicitly have: requires: !cuda  It does not match all cases that do not require cuda. ## Debugging for loops¶ One of the more difficult issues is how to debug for loops when a subset of the arguments are the ones that cause a code crash. The default naming scheme is not always helpful for figuring out the argument combination. For example: > ptmake test s='src/ksp/ksp/tests/ex9.c' i='*1' Using MAKEFLAGS: i=*1 s=src/ksp/ksp/tests/ex9.c TEST arch-osx-pkgs-opt-new/tests/counts/ksp_ksp_tests-ex9_1.counts ok ksp_ksp_tests-ex9_1+pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_type-additive not ok diff-ksp_ksp_tests-ex9_1+pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_type-additive ok ksp_ksp_tests-ex9_1+pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_type-multiplicative ...  In this case, the trick is to use the verbose option, V=1 (or for the shell script workflows, -v) to have it show the commands: > ptmake test s='src/ksp/ksp/tests/ex9.c' i='*1' V=1 Using MAKEFLAGS: V=1 i=*1 s=src/ksp/ksp/tests/ex9.c arch-osx-pkgs-opt-new/tests/ksp/ksp/tests/runex9_1.sh -v ok ksp_ksp_tests-ex9_1+pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_diag_use_amat-0_pc_fieldsplit_type-additive # mpiexec -n 1 ../ex9 -ksp_converged_reason -ksp_error_if_not_converged -pc_fieldsplit_diag_use_amat 0 -pc_fieldsplit_diag_use_amat 0 -pc_fieldsplit_type additive > ex9_1.tmp 2> runex9_1.err ...  This can still be hard to read and pick out what you want. So use the fact that you wantnot ok combined with the fact that # is the delimiter: > ptmake test s='src/ksp/ksp/tests/ex9.c' i='*1' v=1 | grep 'not ok' | cut -d# -f2 mpiexec -n 1 ../ex9 -ksp_converged_reason -ksp_error_if_not_converged -pc_fieldsplit_diag_use_amat 0 -pc_fieldsplit_diag_use_amat 0 -pc_fieldsplit_type multiplicative > ex9_1.tmp 2> runex9_1.err  ## PETSc Test Description Language¶ PETSc tests and tutorials contain within their file a simple language to describe tests and subtests required to run executables associated with compilation of that file. The general skeleton of the file is static char help[] = "A simple MOAB example\n\ ... <source code> ... /*TEST build: requires: moab testset: suffix: 1 requires: !complex testset: suffix: 2 args: -debug -fields v1,v2,v3 test: test: args: -foo bar TEST*/  For our language, a test is associated with the following • A single shell script • A single makefile • A single output file that represents the expected esults Two or more command tests, usually, one or more mpiexec tests that run the executable, and one or more diff tests to compare output with the expected result. Our language also supports a testset that specifies either a new test entirely or multiple executable/diff tests within a single test. At the core, the executable/diff test combination will look something like this: mpiexec -n 1 ../ex1 1> ex1.tmp 2> ex1.err diff ex1.tmp output/ex1.out 1> diff-ex1.tmp 2> diff-ex1.err  In practice, we want to do various logging and counting by the test harness; as are explained further below. The input language supports simple yet flexible test control, and we begin by describing this language. ### Runtime Language Options¶ At the end of each test file, a marked comment block is inserted to describe the test(s) to be run. The elements of the test are done with a set of supported key words that sets up the test. The goals of the language are to be • as minimal as possible with the simplest test requiring only one keyword, • independent of the filename such that a file can be renamed without rewriting the tests, and • intuitive. In order to enable the second goal, the basestring of the filename is defined as the filename without the extension; for example, if the filename is ex1.c, then basestring=ex1. With this background, these keywords are as follows. • testset or test: (Required) • At the top level either a single test or a test set must be specified. All other keywords are sub-entries of this keyword. • suffix: (Optional; Default: suffix="") • The test name is given by testname = basestring if the suffix is set to an empty string, and by testname = basestring + "_" + suffix otherwise. • This can be specified only for top level test nodes. • output_file: (Optional; Default: output_file = "output/" + testname + ".out") • The output of the test is to be compared with an expected result whose name is given by output_file. • This file is described relative to the source directory of the source file and should be in the output subdirectory (for example, output/ex1.out) • nsize: (Optional; Default: nsize=1) • This integer is passed to mpiexec; i.e., mpiexec -n nsize • args: (Optional; Default: "") • These arguments are passed to the executable. • diff_args: (Optional; Default: "") • These arguments are passed to the lib/petsc/bin/petscdiff script that is used in the diff part of the test. For example, -j enables testing the floating point numbers. • TODO: (Optional; Default: False) • Setting this Boolean to True will tell the test to appear in the test harness but report only TODO per the TAP standard. • A runscript will be generated and can easily be modified by hand to run. • filter: (Optional; Default: "") • Sometimes only a subset of the output is meant to be tested against the expected result. If this keyword is used, it processes the executable output and puts it into the file to be actually compared with output_file. • The value of this is the command to be run, for example, grep foo or sort -nr. • If the filter begins with Error:, then the test is assumed to be testing the stderr output, and the error code and output are set up to be tested. • filter_output: (Optional; Default: "") • Sometimes filtering the output file is useful for standardizing tests. For example, in order to handle the issues related to parallel output, both the output from the test example and the output file need to be sorted (since sort does not produce the same output on all machines). This works the same as filter to implement this feature • localrunfiles: (Optional; Default: "") • The tests are run under PETSC_ARCH/tests, but some tests require runtime files that are maintained in the source tree. Files in this (space-delimited) list will be copied over. If you list a directory instead of files, it will copy the entire directory (this is limited currently to a single directory) • The copying is done by the test generator and not by creating makefile dependencies. • requires: (Optional; Default: "") • This is a space-delimited list of run requirements (not build requirements; see Build requirements below). • In general, the language supports and and not constructs using ! => not and , => and. • MPIUNI should work for all -n 1 examples so this need not be in the requirements list. • Inputs sometimes require external matrices that are found in the DATAFILES path. For these tests requires: datafilespath can be specifed. • Packages are indicated with lower-case specification, for example, requires: superlu_dist. • Any defined variable in petscconf.h can be specified with the defined(...) syntax, for example, defined(PETSC_USE_INFO). • Any definition of the form PETSC_HAVE_FOO can just use requires: foo similar to how third-party packages are handled. • timeoutfactor: (Optional; Default: "1") • This parameter allows you to extend the default timeout for an individual test such that the new timeout time is timeout=(default timeout) x (timeoutfactor). • Tests are limited to a set time that is found at the top of "config/petsc_harness.sh" and can be overwritten by passing in the TIMEOUT argument to gmakefile (see ptmake help. ### Additional Specifications¶ In addition to the above keywords, other language features are supported. • for loops: Specifying {{list of values}} will generate a loop over an enclosed space-delimited list of values. It is supported within nsize and args. For example, nsize: {{1 2 4}} args: -matload_block_size {{2 3}}  Here the output for each -matload_block_size value is assumed to give the same output so that only one output file is needed. If the loop causes a different output, then separate output needs to be used: args: -matload_block_size {{2 3}separate output}  In this case, each loop value generates a separate script, and a separate output file is needed. Note that {{...}shared output} is equivalent to {{...}}. See examples below for how it works in practice. ### Test Block Examples¶ The following is the simplest test block: /*TEST test: TEST*/  If this block is in src/a/b/examples/tutorials/ex1.c, then it will create a_b_tutorials-ex1 test that requires only one processor/thread, with no arguments, and diff the resultant output with src/a/b/examples/tutorials/output/ex1.out. For Fortran, the equivalent is !/*TEST ! test: !TEST*/  A more complete example showing just the part within the /*TEST: test: test: suffix: 1 nsize: 2 args: -t 2 -pc_type jacobi -ksp_monitor_short -ksp_type gmres args: -ksp_gmres_cgs_refinement_type refine_always -s2_ksp_type bcgs args: -s2_pc_type jacobi -s2_ksp_monitor_short requires: x  This creates two tests. Assuming that this is src/a/b/examples/tutorials/ex1.c, the tests would be a_b_tutorials-ex1 and a_b_tutorials-ex1_1. Following is an example of how to test a permutuation of arguments against the same output file: testset: suffix: 19 requires: datafilespath args: -f0${DATAFILESPATH}/matrices/poisson1
args: -ksp_type cg -pc_type icc -pc_factor_levels 2
test:
test:
args: -mat_type seqsbaij


Assuming that this is ex10.c, there would be two mpiexec/diff invocations in runex10_19.sh.

Here is a similar example, but the permutation of arguments creates different output:

testset:
requires: datafilespath
args: -f0 ${DATAFILESPATH}/matrices/medium args: -ksp_type bicg test: suffix: 4 args: -pc_type lu test: suffix: 5  Assuming that this is ex10.c, two shell scripts will be created: runex10_4.sh and runex10_5.sh. An example using a for loop is: testset: suffix: 1 args: -f${DATAFILESPATH}/matrices/small -mat_type aij
requires: datafilespath
testset:
suffix: 2
output_file: output/ex138_1.out
args: -f ${DATAFILESPATH}/matrices/small args: -mat_type baij -matload_block_size {{2 3}shared output} requires: datafilespath  In this example, ex138_2 will invoke runex138_2.sh twice with two different arguments, but both are diffed with the same file. Following is an example showing the hierarchical nature of the test specification. testset: suffix:2 output_file: output/ex138_1.out args: -f${DATAFILESPATH}/matrices/small -mat_type baij
test:
test:


This is functionally equivalent to the for loop shown above.

Here is a more complex example using for loops:

testset:
suffix: 19
requires: datafilespath
args: -f0 ${DATAFILESPATH}/matrices/poisson1 args: -ksp_type cg -pc_type icc args: -pc_factor_levels {{0 2 4}separate output} test: test: args: -mat_type seqsbaij  If this is in ex10.c, then the shell scripts generated would be • runex10_19_pc_factor_levels-0.sh • runex10_19_pc_factor_levels-2.sh • runex10_19_pc_factor_levels-4.sh Each shell script would invoke twice. ### Build Language Options¶ You can specify issues related to the compilation of the source file with the build: block. The language is as follows. • requires: (Optional; Default: "") • Same as the runtime requirements (for example, can include requires: fftw) but also requirements related to types: 1. Precision types: single, double, quad, int32 2. Scalar types: complex (and !complex) • In addition, TODO is available to allow you to skip the build of this file but still maintain it in the source tree. • depends: (Optional; Default: "") • List any dependencies required to compile the file A typical example for compiling for only real numbers is /*TEST build: requires: !complex test: TEST*/  ## PETSC Test Harness¶ The goals of the PETSc test harness are threefold. 1. Provide standard output used by other testing tools 2. Be as lightweight as possible and easily fit within the PETSc build chain 3. Provide information on all tests, even those that are not built or run because they do not meet the configuration requirements Before understanding the test harness, you should first understand the desired requirements for reporting and logging. ### Testing the Parsing¶ After inserting the language into the file, you can test the parsing by executing A dictionary will be pretty-printed. From this dictionary printout, any problems in the parsing are is usually obvious. This python file is used by in generating the test harness. ## Test Output Standards: TAP¶ The PETSc test system is designed to be compliant with the Test Anything Protocal (TAP); see https://testanything.org/tap-specification.html This is a simple standard designed to allow testing tools to work together easily. There are libraries to enable the output to be used easily, including sharness, which is used by the git team. However, the simplicity of the PETSc tests and TAP specification means that we use our own simple harness given by a single shell script that each file sources: $PETSC_DIR/config/petsc_harness.sh.

As an example, consider this test input:

test:
suffix: 2
output_file: output/ex138.out
args: -f ${DATAFILESPATH}/matrices/small -mat_type {{aij baij sbaij}} -matload_block_size {{2 3}} requires: datafilespath  A sample output from this would be: ok 1 In mat...tests: "./ex138 -f${DATAFILESPATH}/matrices/small -mat_type aij -matload_block_size 2"
ok 2 In mat...tests: "Diff of ./ex138 -f ${DATAFILESPATH}/matrices/small -mat_type aij -matload_block_size 2" ok 3 In mat...tests: "./ex138 -f${DATAFILESPATH}/matrices/small -mat_type aij -matload_block_size 3"
ok 4 In mat...tests: "Diff of ./ex138 -f ${DATAFILESPATH}/matrices/small -mat_type aij -matload_block_size 3" ok 5 In mat...tests: "./ex138 -f${DATAFILESPATH}/matrices/small -mat_type baij -matload_block_size 2"
ok 6 In mat...tests: "Diff of ./ex138 -f ${DATAFILESPATH}/matrices/small -mat_type baij -matload_block_size 2" ... ok 11 In mat...tests: "./ex138 -f${DATAFILESPATH}/matrices/small -mat_type saij -matload_block_size 2"
ok 12 In mat...tests: "Diff of ./ex138 -f ${DATAFILESPATH}/matrices/small -mat_type aij -matload_block_size 2"  ## Test Harness Implementation¶ Most of the requirements for being TAP-compliant lie in the shell scripts, so we focus on that description. A sample shell script is given the following. #!/bin/sh . petsc_harness.sh petsc_testrun ./ex1 ex1.tmp ex1.err petsc_testrun 'diff ex1.tmp output/ex1.out' diff-ex1.tmp diff-ex1.err petsc_testend  petsc_harness.sh is a small shell script that provides the logging and reporting functions petsc_testrun and petsc_testend. A small sample of the output from the test harness is as follows. ok 1 ./ex1 ok 2 diff ex1.tmp output/ex1.out not ok 4 ./ex2 # ex2: Error: cannot read file not ok 5 diff ex2.tmp output/ex2.out ok 7 ./ex3 -f /matrices/small -mat_type aij -matload_block_size 2 ok 8 diff ex3.tmp output/ex3.out ok 9 ./ex3 -f /matrices/small -mat_type aij -matload_block_size 3 ok 10 diff ex3.tmp output/ex3.out ok 11 ./ex3 -f /matrices/small -mat_type baij -matload_block_size 2 ok 12 diff ex3.tmp output/ex3.out ok 13 ./ex3 -f /matrices/small -mat_type baij -matload_block_size 3 ok 14 diff ex3.tmp output/ex3.out ok 15 ./ex3 -f /matrices/small -mat_type sbaij -matload_block_size 2 ok 16 diff ex3.tmp output/ex3.out ok 17 ./ex3 -f /matrices/small -mat_type sbaij -matload_block_size 3 ok 18 diff ex3.tmp output/ex3.out # FAILED 4 5 # failed 2/16 tests; 87.500% ok  For developers, modifying the lines that get written to the file can be done by modifying ${PETSC_DIR}/config/example_template.py.

To modify the test harness, you can modify \${PETSC_DIR}/config/petsc_harness.sh.

To rerun just the reporting use

config/report_tests.py


To see the full options use

config/report_tests.py -h


To see the full timing information for the five most expensive tests use

config/report_tests.py -t 5