compilation issue

[karthickbrlab]

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]

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 <#74>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UL22BSRS4EHYTKJ7IDZBHFPLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DIOBVGA3DQMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[karthickbrlab]

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
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[BenoitMorel]

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: ‘__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%] 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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 <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UMAD4ABDGFSVU3IH23ZBSIHLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBUGI4DIMJXGE> . You are receiving this because you commented.Message ID: ***@***.***>

[karthickbrlab]

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]

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]

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 <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UPGCWO3DGMUWVB5EN3ZDRXLBAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRUGQ2TENZRGM> . You are receiving this because you commented.Message ID: ***@***.***>

[txfc]

Hello
I also have this problem when running install.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]

I too get similar error after installing gtest and gmock

[BenoitMorel]

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 <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UMU6GAWFF2EPBX6I33ZHJUVLAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRXGE3TMMZRGU> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[txfc]

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]

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... [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! — Reply to this email directly, view it on GitHub <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJJ3UM2JMAF7YNISYS34BDZHUSUHAVCNFSM6AAAAABHML75WKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZRGA3DKMZYHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>