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BenoitMorel / ParGenes

A massively parallel tool for model selection and tree inference on thousands of genes
GNU General Public License v3.0
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compilation issue #74

Open karthickbrlab opened 1 month ago

karthickbrlab commented 1 month ago

Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o

make[2]: *** [src/CMakeFiles/raxml_module.dir/build.make:76: src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o] Error 127

/home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: *** [test/src/CMakeFiles/raxml_test_module.dir/build.make:90: test/src/CMakeFiles/raxml_test_module.dir///src/Checkpoint.cpp.o] Error 127

BenoitMorel commented 1 month ago

Hello, Could you please post the full installation message as well as the command you typed for the installation? Benoit

Le mer. 8 mai 2024 à 09:08, kbsivakumar @.***> a écrit :

make[2]: *** [src/CMakeFiles/raxml_module.dir/build.make:76: src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o] Error 127

/home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: ** [test/src/CMakeFiles/raxml_test_module.dir/build.make:90: test/src/CMakeFiles/raxml_test_module.dir//*/src/Checkpoint.cpp.o] Error 127

— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/74, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UL22BSRS4EHYTKJ7IDZBHFPLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DIOBVGA3DQMA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

karthickbrlab commented 1 month ago

After gitcloned pargenes (base) ubuntu@ubuntu-desktop:~/Documents/ParGenes$ ./install.sh Running from /home/ubuntu/Documents/ParGenes Installing with 4 cores

Installing mpi_scheduler...

-- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found MPI_C: /home/ubuntu/anaconda3/lib/libmpi.so (found version "4.0") -- Found MPI_CXX: /home/ubuntu/anaconda3/lib/libmpicxx.so (found version "4.0") -- Found MPI: TRUE (found version "4.0")
-- WITH MPI -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5")
-- WITH OPENMP -- Configuring done -- Generating done -- Build files have been written to: /home/ubuntu/Documents/ParGenes/MPIScheduler/build [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Checkpoint.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/main.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Command.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/CommandsRunner.cpp.o [ 35%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Common.cpp.o [ 42%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/DynamicLibrary.cpp.o [ 50%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Instance.cpp.o [ 57%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/ParallelImplementation.cpp.o [ 64%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/RunStatistics.cpp.o [ 71%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/SVGDrawer.cpp.o [ 78%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/fork_implem/ForkImplem.cpp.o [ 85%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/split_implem/SplitImplem.cpp.o [ 92%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/onecore_implem/OneCoreImplem.cpp.o /home/ubuntu/Documents/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp: In member function ‘int MPIScheduler::SplitSlave::doWork(MPIScheduler::CommandPtr, MPI_Comm, const string&)’: /home/ubuntu/Documents/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp:101:65: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 101 | int res = library->run(logsFile, errFile, command->getArgs(), (void*)raxmlComm); | ^~~~ [100%] Linking CXX executable ../mpi-scheduler [100%] Built target mpi-scheduler

Installing raxml-ng library ...

-- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler: GNU 11.4.0 => /usr/bin/c++ -- Building RELEASE -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Using flags: -std=c++11 -Wall -Wextra -D_RAXML_PTHREADS -pthread -D_RAXML_BUILD_AS_LIB -fPIC -- Building dependencies in: /home/ubuntu/Documents/ParGenes/raxml-ng/build/localdeps CMake Deprecation Warning at libs/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at libs/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Disable sse2neon simd, because not supported -- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false -- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false -- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false -- Libpll static build enabled -- pll_static CMake Deprecation Warning at libs/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Found MPI_C: /home/ubuntu/anaconda3/lib/libmpi.so (found version "4.0") -- Found MPI_CXX: /home/ubuntu/anaconda3/lib/libmpicxx.so (found version "4.0") -- Found MPI: TRUE (found version "4.0")
-- RAxML-NG will be built as a library. -- Found GTest: /home/ubuntu/anaconda3/lib/cmake/GTest/GTestConfig.cmake (found version "1.10.0")
-- Building tests -- Configuring done -- Generating done -- Build files have been written to: /home/ubuntu/Documents/ParGenes/raxml-ng/build [ 0%] [BISON][parse_utree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 168 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 168 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:170.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 170 | %destructor { pll_utree_graph_destroy($$,NULL); } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:171.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 171 | %destructor { free($$); } STRING | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:172.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 172 | %destructor { free($$); } NUMBER | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:173.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 173 | %destructor { free($$); } label | ^~~ [ 2%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir//pllmod_common.c.o [ 2%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir//pllmod_common.c.o [ 2%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir//pllmod_common.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 3%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4 [ 4%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4 [ 6%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/binary_io_operations.c.o [ 6%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/lbfgsb.c.o [ 6%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_callback.c.o [ 6%] [BISON][parse_rtree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 106 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 106 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:108.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 108 | %destructor { pll_rtree_graph_destroy($$,NULL); } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:109.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 109 | %destructor { free($$); } STRING | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:110.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 110 | %destructor { free($$); } NUMBER | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:111.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 111 | %destructor { free($$); } label | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 6%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o [ 6%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/pll_binary.c.o [ 7%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linesearch.c.o [ 7%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_search.c.o [ 7%] Built target pllmodbinary_obj [ 8%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linpack.c.o [ 8%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/__/pllmod_common.c.o [ 9%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/pll_msa.c.o [ 9%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/miniCBLAS.c.o [ 10%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/pllmod_algorithm.c.o [ 11%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o [ 12%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/subalgorithms.c.o [ 12%] Built target pllmodmsa_obj [ 13%] [BISON][split_utree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 76 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 76 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:79.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 79 | %destructor { } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 14%] [FLEX][lex_split_t] Building scanner with flex 2.6.4 [ 14%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/consensus.c.o [ 14%] Built target pllmodalgorithm_obj [ 15%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir//pllmod_common.c.o [ 15%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models.c.o [ 15%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/opt_algorithms.c.o [ 15%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c: In function ‘pllmod_utree_weight_consensus’: /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:465:48: warning: ‘ [tree #’ directive output may be truncated writing 8 bytes into a region of size between 1 and 200 [-Wformat-truncation=] 465 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:465:45: note: directive argument in the range [1, 4294967295] 465 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~~~~ In file included from /usr/include/stdio.h:894, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/pll.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/pll_tree.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘builtin___snprintf_chk’ output between 11 and 219 bytes into a destination of size 200 71 | return builtin_snprintf_chk (s, n, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~ 72 | glibc_objsize (s), fmt, | ~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~ [ 16%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_aa.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c: In function ‘pllmod_utree_consensus’: /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:607:48: warning: ‘ [tree #’ directive output may be truncated writing 8 bytes into a region of size between 1 and 200 [-Wformat-truncation=] 607 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~ In file included from /usr/include/stdio.h:894, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/pll.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/pll_tree.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘builtin_snprintf_chk’ output between 11 and 219 bytes into a destination of size 200 71 | return builtin_snprintf_chk (s, n, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~ 72 | glibc_objsize (s), fmt, | ~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~ [ 17%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/pll_tree.c.o [ 18%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_dna.c.o [ 18%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_gt.c.o [ 19%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/pll_optimize.c.o [ 20%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_mult.c.o [ 20%] Built target pllmodutil_obj [ 21%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o [ 22%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o [ 22%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/rtree_operations.c.o [ 23%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tree_hashtable.c.o [ 23%] Built target pllmodoptimize_obj [ 23%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o [ 23%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/treeinfo.c.o [ 24%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o [ 24%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o [ 25%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_distances.c.o [ 26%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o [ 26%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tbe_functions.c.o [ 26%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/derivatives.c.o [ 27%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fasta.c.o [ 27%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony.c.o [ 28%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_operations.c.o [ 29%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_constraint.c.o [ 29%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/split_utree.c.o [ 30%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/gamma.c.o [ 31%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/lex_split.c.o [ 32%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/hardware.c.o [ 32%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/likelihood.c.o [ 32%] Built target pllmodtree_obj [ 33%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/list.c.o [ 33%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/maps.c.o [ 34%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/models.c.o [ 34%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/output.c.o [ 35%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parsimony.c.o [ 36%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/partials.c.o [ 36%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/phylip.c.o [ 37%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/pll.c.o [ 37%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/random.c.o [ 38%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/repeats.c.o [ 38%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/rtree.c.o [ 39%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/stepwise.c.o [ 39%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree.c.o [ 40%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_moves.c.o [ 41%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_svg.c.o [ 41%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_sse.c.o [ 42%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_sse.c.o [ 42%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_sse.c.o [ 43%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_sse.c.o [ 43%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_sse.c.o [ 44%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx.c.o [ 45%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx.c.o [ 45%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx.c.o [ 46%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx.c.o [ 46%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx.c.o [ 47%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx2.c.o [ 47%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx2.c.o [ 48%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx2.c.o [ 48%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx2.c.o [ 49%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx2.c.o [ 49%] Built target pll_obj [ 50%] Linking C static library libpll.a [ 50%] Built target pll_static [ 51%] Linking C static library libpllmodalgorithm.a [ 51%] Linking C static library libpllmodoptimize.a [ 51%] Linking C static library libpllmodmsa.a [ 51%] Linking C static library libpllmodbinary.a [ 51%] Built target pllmodmsa_static [ 51%] Built target pllmodalgorithm_static [ 51%] Built target pllmodbinary_static [ 51%] Built target pllmodoptimize_static [ 51%] Linking C static library libpllmodtree.a [ 51%] Linking C static library libpllmodutil.a [ 51%] Built target pllmodutil_static [ 51%] Built target pllmodtree_static [ 53%] Building CXX object src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o [ 54%] Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o [ 54%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/AncestralStates.cpp.o [ 54%] Building CXX object src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [src/CMakeFiles/raxml_module.dir/build.make:104: src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o] Error 127 make[2]: Waiting for unfinished jobs.... make[2]: [src/CMakeFiles/raxml_module.dir/build.make:90: src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o] Error 127 make[2]: [src/CMakeFiles/raxml_module.dir/build.make:76: src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o] Error 127 make[1]: [CMakeFiles/Makefile2:692: src/CMakeFiles/raxml_module.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: *** [test/src/CMakeFiles/raxml_test_module.dir/build.make:76: test/src/CMakeFiles/raxml_test_module.dir///src/AncestralStates.cpp.o] Error 127 make[2]: *** Waiting for unfinished jobs.... [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/ICScoreCalculator.cpp.o [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/Checkpoint.cpp.o [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir//__/src/CommandLineParser.cpp.o /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:118: test/src/CMakeFiles/raxml_test_module.dir///src/ICScoreCalculator.cpp.o] Error 127 /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:90: test/src/CMakeFiles/raxml_test_module.dir///src/Checkpoint.cpp.o] Error 127 make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:104: test/src/CMakeFiles/raxml_test_module.dir///src/CommandLineParser.cpp.o] Error 127 make[1]: [CMakeFiles/Makefile2:724: test/src/CMakeFiles/raxml_test_module.dir/all] Error 2 make: *** [Makefile:146: all] Error 2

BenoitMorel commented 1 month ago

Hello, Sorry for the late reply. Please try installing: conda install gxx_linux-64

Le ven. 10 mai 2024 à 11:35, kbsivakumar @.***> a écrit :

After gitcloned pargenes (base) @.***:~/Documents/ParGenes$ ./install.sh Running from /home/ubuntu/Documents/ParGenes Installing with 4 cores

Installing mpi_scheduler...

-- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found MPI_C: /home/ubuntu/anaconda3/lib/libmpi.so (found version "4.0") -- Found MPI_CXX: /home/ubuntu/anaconda3/lib/libmpicxx.so (found version "4.0") -- Found MPI: TRUE (found version "4.0") -- WITH MPI -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- WITH OPENMP -- Configuring done -- Generating done -- Build files have been written to: /home/ubuntu/Documents/ParGenes/MPIScheduler/build [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Checkpoint.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/main.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Command.cpp.o [ 28%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/CommandsRunner.cpp.o [ 35%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Common.cpp.o [ 42%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/DynamicLibrary.cpp.o [ 50%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Instance.cpp.o [ 57%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/ParallelImplementation.cpp.o [ 64%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/RunStatistics.cpp.o [ 71%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/SVGDrawer.cpp.o [ 78%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/fork_implem/ForkImplem.cpp.o [ 85%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/split_implem/SplitImplem.cpp.o [ 92%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/onecore_implem/OneCoreImplem.cpp.o /home/ubuntu/Documents/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp: In member function ‘int MPIScheduler::SplitSlave::doWork(MPIScheduler::CommandPtr, MPI_Comm, const string&)’: /home/ubuntu/Documents/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp:101:65: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 101 | int res = library->run(logsFile, errFile, command->getArgs(), (void*)raxmlComm); | ^~~~ [100%] Linking CXX executable ../mpi-scheduler [100%] Built target mpi-scheduler

Installing raxml-ng library ...

-- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler: GNU 11.4.0 => /usr/bin/c++ -- Building RELEASE -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Using flags: -std=c++11 -Wall -Wextra -D_RAXML_PTHREADS -pthread -D_RAXML_BUILD_AS_LIB -fPIC -- Building dependencies in: /home/ubuntu/Documents/ParGenes/raxml-ng/build/localdeps CMake Deprecation Warning at libs/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at libs/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "3.8.2") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Disable sse2neon simd, because not supported -- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false -- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false -- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false -- Libpll static build enabled -- pll_static CMake Deprecation Warning at libs/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Found MPI_C: /home/ubuntu/anaconda3/lib/libmpi.so (found version "4.0") -- Found MPI_CXX: /home/ubuntu/anaconda3/lib/libmpicxx.so (found version "4.0") -- Found MPI: TRUE (found version "4.0") -- RAxML-NG will be built as a library. -- Found GTest: /home/ubuntu/anaconda3/lib/cmake/GTest/GTestConfig.cmake (found version "1.10.0") -- Building tests -- Configuring done -- Generating done -- Build files have been written to: /home/ubuntu/Documents/ParGenes/raxml-ng/build [ 0%] [BISON][parse_utree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 168 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:168.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 168 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:170.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 170 | %destructor { pll_utree_graph_destroy($$,NULL); } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:171.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 171 | %destructor { free($$); } STRING | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:172.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 172 | %destructor { free($$); } NUMBER | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:173.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 173 | %destructor { free($$); } label | ^~~ [ 2%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/ /pllmod_common.c.o [ 2%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/ /pllmod_common.c.o [ 2%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/

/pllmod_common.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 3%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4 [ 4%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4 [ 6%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/binary_io_operations.c.o [ 6%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/lbfgsb.c.o [ 6%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_callback.c.o [ 6%] [BISON][parse_rtree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 106 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:106.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 106 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:108.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 108 | %destructor { pll_rtree_graph_destroy($$,NULL); } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:109.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 109 | %destructor { free($$); } STRING | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:110.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 110 | %destructor { free($$); } NUMBER | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y:111.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 111 | %destructor { free($$); } label | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/parse_rtree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 6%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o [ 6%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/pll_binary.c.o [ 7%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linesearch.c.o [ 7%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_search.c.o [ 7%] Built target pllmodbinary_obj [ 8%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linpack.c.o [ 8%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir//pllmod_common.c.o [ 9%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/pll_msa.c.o [ 9%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/miniCBLAS.c.o [ 10%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/pllmod_algorithm.c.o [ 11%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o [ 12%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/subalgorithms.c.o [ 12%] Built target pllmodmsa_obj [ 13%] [BISON][split_utree_t] Building parser with bison 3.8.2 /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: POSIX Yacc does not support %error-verbose [-Wyacc] 76 | %error-verbose | ^~~~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:76.1-14: warning: deprecated directive: ‘%error-verbose’, use ‘%define parse.error verbose’ [-Wdeprecated] 76 | %error-verbose | ^~~~~~ | %define parse.error verbose /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y:79.1-11: warning: POSIX Yacc does not support %destructor [-Wyacc] 79 | %destructor { } subtree | ^~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/split_utree.y: warning: fix-its can be applied. Rerun with option '--update'. [-Wother] [ 14%] [FLEX][lex_split_t] Building scanner with flex 2.6.4 [ 14%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/consensus.c.o [ 14%] Built target pllmodalgorithm_obj [ 15%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir//pllmod_common.c.o [ 15%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models.c.o [ 15%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/opt_algorithms.c.o [ 15%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c: In function ‘pllmod_utree_weight_consensus’: /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:465:48: warning: ‘ [tree #’ directive output may be truncated writing 8 bytes into a region of size between 1 and 200 [-Wformat-truncation=] 465 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~ /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:465:45: note: directive argument in the range [1, 4294967295] 465 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~~~~ In file included from /usr/include/stdio.h:894, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/pll.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/pll_tree.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘_builtinsnprintf_chk’ output between 11 and 219 bytes into a destination of size 200 71 | return __builtin___snprintf_chk (

*s, n, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~ 72 | glibc_objsize (s), fmt, | ~~~~~~~~~ 73 | va_arg_pack ()); | ~~~~~ [ 16%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_aa.c.o /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c: In function ‘pllmod_utree_consensus’: /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:607:48: warning: ‘ [tree #’ directive output may be truncated writing 8 bytes into a region of size between 1 and 200 [-Wformat-truncation=] 607 | snprintf(pll_errmsg, PLLMOD_ERRMSG_LEN, "%s [tree #%u]", | ^~~~ In file included from /usr/include/stdio.h:894, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/libs/libpll/src/pll.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/pll_tree.h:26, from /home/ubuntu/Documents/ParGenes/raxml-ng/libs/pll-modules/src/tree/consensus.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:71:10: note: ‘builtin_snprintfchk’ output between 11 and 219 bytes into a destination of size 200 71 | return builtinsnprintf_chk (s, n, USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~ 72 | glibc_objsize (s), fmt, | ~~~~~~~~~ 73 | va_arg_pack ()); | ~~~~~ [ 17%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/pll_tree.c.o [ 18%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_dna.c.o [ 18%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_gt.c.o [ 19%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/pll_optimize.c.o [ 20%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_mult.c.o [ 20%] Built target pllmodutil_obj [ 21%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o [ 22%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o [ 22%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/rtree_operations.c.o [ 23%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tree_hashtable.c.o [ 23%] Built target pllmodoptimize_obj [ 23%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o [ 23%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/treeinfo.c.o [ 24%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o [ 24%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o [ 25%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_distances.c.o [ 26%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o [ 26%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tbe_functions.c.o [ 26%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/derivatives.c.o [ 27%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fasta.c.o [ 27%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony.c.o [ 28%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_operations.c.o [ 29%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_constraint.c.o [ 29%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/split_utree.c.o [ 30%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/gamma.c.o [ 31%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/lex_split.c.o [ 32%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/hardware.c.o [ 32%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/likelihood.c.o [ 32%] Built target pllmodtree_obj [ 33%] Building C object 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C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/stepwise.c.o [ 39%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree.c.o [ 40%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_moves.c.o [ 41%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_svg.c.o [ 41%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_sse.c.o [ 42%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_sse.c.o [ 42%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_sse.c.o [ 43%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_sse.c.o [ 43%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_sse.c.o [ 44%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx.c.o [ 45%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx.c.o [ 45%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx.c.o [ 46%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx.c.o [ 46%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx.c.o [ 47%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx2.c.o [ 47%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx2.c.o [ 48%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx2.c.o [ 48%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx2.c.o [ 49%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx2.c.o [ 49%] Built target pll_obj [ 50%] Linking C static library libpll.a [ 50%] Built target pll_static [ 51%] Linking C static library libpllmodalgorithm.a [ 51%] Linking C static library libpllmodoptimize.a [ 51%] Linking C static library libpllmodmsa.a [ 51%] Linking C static library libpllmodbinary.a [ 51%] Built target pllmodmsa_static [ 51%] Built target pllmodalgorithm_static [ 51%] Built target pllmodbinary_static [ 51%] Built target pllmodoptimize_static [ 51%] Linking C static library libpllmodtree.a [ 51%] Linking C static library libpllmodutil.a [ 51%] Built target pllmodutil_static [ 51%] Built target pllmodtree_static [ 53%] Building CXX object src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o [ 54%] Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o [ 54%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/AncestralStates.cpp.o [ 54%] Building CXX object src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [src/CMakeFiles/raxml_module.dir/build.make:104: src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o] Error 127 make[2]: Waiting for unfinished jobs.... make[2]: [src/CMakeFiles/raxml_module.dir/build.make:90: src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o] Error 127 make[2]: [src/CMakeFiles/raxml_module.dir/build.make:76: src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o] Error 127 make[1]: [CMakeFiles/Makefile2:692: src/CMakeFiles/raxml_module.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:76: test/src/CMakeFiles/raxml_test_module.dir///src/AncestralStates.cpp.o] Error 127 make[2]: Waiting for unfinished jobs.... [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/ICScoreCalculator.cpp.o [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/Checkpoint.cpp.o [ 55%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/CommandLineParser.cpp.o /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:118: test/src/CMakeFiles/raxml_test_module.dir///src/ICScoreCalculator.cpp.o] Error 127 /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found /home/ubuntu/anaconda3/bin/mpicxx: line 328: x86_64-conda-linux-gnu-c++: command not found make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:90: test/src/CMakeFiles/raxml_test_module.dir///src/Checkpoint.cpp.o] Error 127 make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:104: test/src/CMakeFiles/raxml_test_module.dir///src/CommandLineParser.cpp.o] Error 127 make[1]: ** [CMakeFiles/Makefile2:724: test/src/CMakeFiles/raxml_test_module.dir/all] Error 2 make: [Makefile:146: all] Error 2

— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/74#issuecomment-2104284171, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UMAD4ABDGFSVU3IH23ZBSIHLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUGI4DIMJXGE . You are receiving this because you commented.Message ID: @.***>

karthickbrlab commented 1 month ago

HI..It resolved that error. Yet, kindly look into this one.

[ 96%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/util/parseutil.cpp.o [ 96%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir///src/util/sysutil.cpp.o [ 97%] Building CXX object test/src/CMakeFiles/raxml_test_module.dir/CommandLineParserTest.cpp.o In file included from /home/ubuntu/Documents/ParGenes/raxml-ng/test/src/CommandLineParserTest.cpp:1: /home/ubuntu/Documents/ParGenes/raxml-ng/test/src/RaxmlTest.hpp:3:10: fatal error: gtest/gtest.h: No such file or directory 3 | #include <gtest/gtest.h> | ^~~~~~~ compilation terminated. make[2]: [test/src/CMakeFiles/raxml_test_module.dir/build.make:622: test/src/CMakeFiles/raxml_test_module.dir/CommandLineParserTest.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... make[1]: [CMakeFiles/Makefile2:724: test/src/CMakeFiles/raxml_test_module.dir/all] Error 2 make: [Makefile:146: all] Error 2

nylander commented 1 month ago

Dear @karthickbrlab ,

during the build of raxml-ng, the file gtest.h can not be found (missing or placed in an unexpected location). Since you run the installation in a conda environment, you may try*

$ conda install gmock gtest -c conda-forge

And re-run the ParPenes installation script.

* Note: untested by me

BenoitMorel commented 1 month ago

Thank you very much Johan, that's also what I would try. If that doesn't work I'll try to find the flag to disable the test compilation in raxml.

Le mer. 22 mai 2024 à 12:28, Johan Nylander @.***> a écrit :

Dear @karthickbrlab https://github.com/karthickbrlab ,

during the build of raxml-ng, the file gtest.h can not be found (missing or placed in an unexpected location). Since you run the installation in a conda environment, you may try*

$ conda install gmock gtest -c conda-forge

And re-run the ParPenes installation script.

  • Note: untested by me

— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/74#issuecomment-2124452713, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UPGCWO3DGMUWVB5EN3ZDRXLBAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRUGQ2TENZRGM . You are receiving this because you commented.Message ID: @.***>

txfc commented 3 weeks ago

Hello I also have this problem when runninginstall.sh. I have installed gtest and gmock by conda after that error. But it does not work.

In file included from /bio_softer/ParGenes/raxml-ng/test/src/CommandLineParserTest.cpp:1:
/bio_softer/ParGenes/raxml-ng/test/src/RaxmlTest.hpp:3:10: fatal error: gtest/gtest.h: No such file or directory
    3 | #include <gtest/gtest.h>
      |          ^~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [test/src/CMakeFiles/raxml_test_module.dir/build.make:622: test/src/CMakeFiles/raxml_test_module.dir/CommandLineParserTest.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:724: test/src/CMakeFiles/raxml_test_module.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

/usr/bin/cmake: /home/miniconda3/lib/libcurl.so.4: no version information available (required by /usr/bin/cmake)
[ 97%] Linking CXX shared module ../../bin/raxml-ng.so
/usr/bin/cmake: /home/miniconda3/lib/libcurl.so.4: no version information available (required by /usr/bin/cmake)
/usr/bin/cmake: /home/miniconda3/lib/libcurl.so.4: no version information available (required by /usr/bin/cmake)
[ 97%] Built target raxml_module
make: *** [Makefile:146: all] Error 2

@BenoitMorel Do you have any alternative solutions? Thank you.

karthickbrlab commented 3 weeks ago

I too get similar error after installing gtest and gmock

BenoitMorel commented 2 weeks ago

Hello, In ParGenes repository, try to remove the two last lines of raxml-ng/CMakeLists.txt: enable_testing() add_subdirectory(${PROJECT_SOURCE_DIR}/test/src)

Let me know if that works Benoit

Le ven. 14 juin 2024 à 06:13, kbsivakumar @.***> a écrit :

I too get similar error after installing gtest and gmock

— Reply to this email directly, view it on GitHub https://github.com/BenoitMorel/ParGenes/issues/74#issuecomment-2167176315, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJJ3UMU6GAWFF2EPBX6I33ZHJUVLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRXGE3TMMZRGU . You are receiving this because you were mentioned.Message ID: @.***>

txfc commented 2 weeks ago

Hello, I removed the last two lines as you said. But I get a different error.

** Installing ASTER...                 **
******************************************
g++ -v 2>&1 | tail -n 1
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)
echo 'If installation failed, please ensure g++ version >= 7.5.0'
If installation failed, please ensure g++ version >= 7.5.0
mkdir -p bin
g++ -std=gnu++11 -march=native -Ofast -pthread src/astral.cpp -o bin/astral || g++ -std=c++17 -O2 -pthread src/astral.cpp -o bin/astral
g++ -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro || g++ -std=c++17 -O2 -pthread src/astral-pro.cpp -o bin/astral-pro
g++ -std=gnu++11 -march=native -Ofast -pthread src/astral-hybrid.cpp -o bin/astral-hybrid || g++ -std=c++17 -O2 -pthread src/astral-hybrid.cpp -o bin/astral-hybrid
g++ -std=gnu++11 -march=native -Ofast -pthread src/caster-site.cpp -o bin/caster-site || g++ -std=gnu++17 -O2 -pthread src/caster-site.cpp -o bin/caster-site
g++ -std=gnu++11 -march=native -D CUSTOMIZED_ANNOTATION_TERMINAL_LENGTH -Ofast -pthread src/caster-site.cpp -o bin/caster-site_branchlength || g++ -std=gnu++17 -D CUSTOMIZED_ANNOTATION_TERMINAL_LENGTH -O2 -pthread src/caster-site.cpp -o bin/caster-site_branchlength
g++ -std=gnu++11 -march=native -Ofast -pthread src/caster-pair.cpp -o bin/caster-pair || g++ -std=gnu++17 -O2 -pthread src/caster-pair.cpp -o bin/caster-pair
g++ -std=gnu++11 -march=native -Ofast -pthread src/waster-site.cpp -o bin/waster-site || g++ -std=gnu++17 -O2 -pthread src/waster-site.cpp -o bin/waster-site
echo "*** Installation complete! ***"
*** Installation complete! ***

Copying all binaries into /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r MPIScheduler/build/mpi-scheduler /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r raxml-ng/bin/raxml-ng /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r modeltest/bin/modeltest-ng /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r raxml-ng/bin/raxml-ng-mpi.so /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp: cannot stat 'raxml-ng/bin/raxml-ng-mpi.so': No such file or directory
cp -r modeltest/build/src/modeltest-ng-mpi.so /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp: cannot stat 'modeltest/build/src/modeltest-ng-mpi.so': No such file or directory
cp -r ASTRAL/Astral/astral.jar /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r ASTRAL/Astral/lib /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r ASTER/bin/astral /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r ASTER/bin/astral-pro /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries
cp -r ASTER/bin/astral-hybrid /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries

Running unit tests...
[help]: [ml_search_pargenes]: Success!
[modeltest_pargenes]: Success!
[bootstraps_pargenes]: Success!
[astral_pargenes]: Success!
[aster_pargenes]: Success!
[all_pargenes]: Success!
[all_aster_pargenes]: Success!
[ml_search_pargenes-hpc]: Not trying to print report file
Test failed, restarting with logs enabled and continue option
after parse:
########################
#    PARGENES v1.2.0   #
########################

2024-06-16 04:41:28.819964
ParGenes was called as follow:
/mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py -a /mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files -o /mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc -r /mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt -c 4 -s 3 -p 3 --continue --scheduler split

[0:00:00] end of MSAs initializations
Binaries directory: /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_src/../pargenes_binaries
Error in run_scheduler: the binary /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_src/../pargenes_binaries/raxml-ng-mpi.so does not exist. Please check your installation
Writing report file in /mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc/report.txt
When reporting the issue, please always send us this file.
Traceback (most recent call last):
  File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 121, in run_command
    subprocess.check_call(shlex.split(command), stdout = out)
  File "/home/genetic/miniconda3/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['python', '/mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py', '-a', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files', '-o', '/mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc', '-r', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt', '-c', '4', '-s', '3', '-p', '3']' returned non-zero exit status 238.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 272, in <module>
    failures += test_ml_search(pargenes_script)
  File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 153, in test_ml_search
    run_command(command, "ml_search_" + basename, output)
  File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 134, in run_command
    subprocess.check_call(shlex.split(command + " --continue"))
  File "/home/genetic/miniconda3/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['python', '/mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py', '-a', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files', '-o', '/mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc', '-r', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt', '-c', '4', '-s', '3', '-p', '3', '--continue']' returned non-zero exit status 238.

however, I have installed mpi and open-mpi by conda. I do not know what happened. I tried to run pargenes.py, and it worked. I only have a machine with 256 cores. Is it essential for me to run pargenes-hpc.py? Will I take full advantage of my multi-core performance by running pargenes.py? Thank you!

BenoitMorel commented 2 weeks ago

Hi, That's weird, given that you have mpi installed. But as you said, if you have one single machine, and if the "normal" pargenes works, you don't need pargenes-hpc. Best, Benoit

Le dim. 16 juin 2024 à 07:59, txfc @.***> a écrit :

Hello, I removed the last two lines as you said. But I get a different error.

Installing ASTER...

g++ -v 2>&1 | tail -n 1 gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04) echo 'If installation failed, please ensure g++ version >= 7.5.0' If installation failed, please ensure g++ version >= 7.5.0 mkdir -p bin g++ -std=gnu++11 -march=native -Ofast -pthread src/astral.cpp -o bin/astral || g++ -std=c++17 -O2 -pthread src/astral.cpp -o bin/astral g++ -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro || g++ -std=c++17 -O2 -pthread src/astral-pro.cpp -o bin/astral-pro g++ -std=gnu++11 -march=native -Ofast -pthread src/astral-hybrid.cpp -o bin/astral-hybrid || g++ -std=c++17 -O2 -pthread src/astral-hybrid.cpp -o bin/astral-hybrid g++ -std=gnu++11 -march=native -Ofast -pthread src/caster-site.cpp -o bin/caster-site || g++ -std=gnu++17 -O2 -pthread src/caster-site.cpp -o bin/caster-site g++ -std=gnu++11 -march=native -D CUSTOMIZED_ANNOTATION_TERMINAL_LENGTH -Ofast -pthread src/caster-site.cpp -o bin/caster-site_branchlength || g++ -std=gnu++17 -D CUSTOMIZED_ANNOTATION_TERMINAL_LENGTH -O2 -pthread src/caster-site.cpp -o bin/caster-site_branchlength g++ -std=gnu++11 -march=native -Ofast -pthread src/caster-pair.cpp -o bin/caster-pair || g++ -std=gnu++17 -O2 -pthread src/caster-pair.cpp -o bin/caster-pair g++ -std=gnu++11 -march=native -Ofast -pthread src/waster-site.cpp -o bin/waster-site || g++ -std=gnu++17 -O2 -pthread src/waster-site.cpp -o bin/waster-site echo " Installation complete! " Installation complete!

Copying all binaries into /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r MPIScheduler/build/mpi-scheduler /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r raxml-ng/bin/raxml-ng /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r modeltest/bin/modeltest-ng /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r raxml-ng/bin/raxml-ng-mpi.so /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp: cannot stat 'raxml-ng/bin/raxml-ng-mpi.so': No such file or directory cp -r modeltest/build/src/modeltest-ng-mpi.so /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp: cannot stat 'modeltest/build/src/modeltest-ng-mpi.so': No such file or directory cp -r ASTRAL/Astral/astral.jar /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r ASTRAL/Astral/lib /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r ASTER/bin/astral /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r ASTER/bin/astral-pro /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries cp -r ASTER/bin/astral-hybrid /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_binaries

Running unit tests...

[ml_search_pargenes-hpc]: Not trying to print report file Test failed, restarting with logs enabled and continue option after parse: ########################

PARGENES v1.2.0

########################

2024-06-16 04:41:28.819964 ParGenes was called as follow: /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py -a /mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files -o /mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc -r /mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt -c 4 -s 3 -p 3 --continue --scheduler split

[0:00:00] end of MSAs initializations Binaries directory: /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_src/../pargenes_binaries Error in run_scheduler: the binary /mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes_src/../pargenes_binaries/raxml-ng-mpi.so does not exist. Please check your installation Writing report file in /mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc/report.txt When reporting the issue, please always send us this file. Traceback (most recent call last): File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 121, in run_command subprocess.check_call(shlex.split(command), stdout = out) File "/home/genetic/miniconda3/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['python', '/mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py', '-a', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files', '-o', '/mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc', '-r', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt', '-c', '4', '-s', '3', '-p', '3']' returned non-zero exit status 238.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 272, in failures += test_ml_search(pargenes_script) File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 153, in test_ml_search run_command(command, "mlsearch" + basename, output) File "/mnt/data/genetic/bio_softer/ParGenes/tests/run_tests.py", line 134, in run_command subprocess.check_call(shlex.split(command + " --continue")) File "/home/genetic/miniconda3/lib/python3.10/subprocess.py", line 369, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['python', '/mnt/data/genetic/bio_softer/ParGenes/pargenes/pargenes-hpc.py', '-a', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/fasta_files', '-o', '/mnt/data/genetic/bio_softer/ParGenes/tests/tests_outputs/test_ml_search/pargenes-hpc', '-r', '/mnt/data/genetic/bio_softer/ParGenes/tests/smalldata/raxml_global_options.txt', '-c', '4', '-s', '3', '-p', '3', '--continue']' returned non-zero exit status 238.

however, I have installed mpi and open-mpi by conda. I do not know what happened. I tried to run pargenes.py, and it worked. I only have a machine with 256 cores. Is it essential for me to run pargenes-hpc.py? Will I take full advantage of my multi-core performance by running pargenes.py? Thank you!

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