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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
42 stars 6 forks source link

Not reading MPI #63

Closed tdnavarrom closed 5 years ago

tdnavarrom commented 5 years ago

Hello, I am an unable to run pargenes-hpc.py, the log file says 

"Invalid scheduler implementation: --split-scheduler
Error: trying to use an MPI implementation that was not compiled"

I would like to know if you know how to fix that, I am using mpich2 v3.2, gcc 5.40 and Python 3.7, I have mpich2 compiled. Also, pargenes.py runs without problems

BenoitMorel commented 5 years ago

Hello Tomas, Did you install with install.sh script? Can you send me the logs from the installation? It looks like the compilation failed to detect your mpi installation. I will have a look on Monday when I am back from vacations :) Benoit

Le mer. 30 oct. 2019 à 16:37, Tomas Navarro notifications@github.com a écrit :

Hello, I am an unable to run pargenes-hpc.py, the log file says

"Invalid scheduler implementation: --split-scheduler Error: trying to use an MPI implementation that was not compiled" `` I would like to know if you know how to fix that, I am using mpich2 v3.2, gcc 5.40 and Python 3.7, I have mpich2 compiled. Also, pargenes.py runs without problems

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tdnavarrom commented 5 years ago

Hello, yes I did, and may I know which are the log files from the installation?

BenoitMorel commented 5 years ago

I mean everything that is printed in the console when you run the script

Le mer. 30 oct. 2019 à 21:45, Tomas Navarro notifications@github.com a écrit :

Hello, yes I did, and may I know which are the log files from the installation?

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tdnavarrom commented 5 years ago

`./install.sh Installing with 4 cores

Installing mpi_scheduler...

-- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found MPI_C: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- Found MPI_CXX: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpicxx.so;/share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- WITH MPI -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
-- WITH OPENMP -- Configuring done -- Generating done -- Build files have been written to: /home/tdnavarrom/ParGenes/MPIScheduler/build Scanning dependencies of target mpi-scheduler [ 14%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/main.cpp.o [ 21%] Building CXX object src/CMakeFiles/mpi-scheduler.dir/Checkpoint.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/tdnavarrom/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp: In member function ‘int MPIScheduler::SplitSlave::doWork(MPIScheduler::CommandPtr, MPI_Comm, const string&)’: /home/tdnavarrom/ParGenes/MPIScheduler/src/split_implem/SplitImplem.cpp:101:72: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 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 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler: GNU 5.4.0 => /share/apps/gcc/5.4.0/bin/g++ -- Building RELEASE -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Using flags: -std=c++11 -Wall -Wextra -D_RAXML_PTHREADS -pthread -D_RAXML_BUILD_AS_LIB -fPIC -- Building dependencies in: /home/tdnavarrom/ParGenes/raxml-ng/build/localdeps -- pll-modules static build enabled -- Found BISON: /usr/bin/bison (found version "2.4.1") -- Found FLEX: /usr/bin/flex (found version "2.5.35") -- 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 -- 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: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- Found MPI_CXX: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpicxx.so;/share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- RAxML-NG will be built as a library. -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY) -- GTest not found CMake Warning at test/src/CMakeLists.txt:5 (message): Skipping building tests.

-- Configuring done -- Generating done -- Build files have been written to: /home/tdnavarrom/ParGenes/raxml-ng/build Scanning dependencies of target pllmodbinary_obj Scanning dependencies of target pllmodoptimize_obj Scanning dependencies of target pllmodalgorithm_obj [ 1%] [FLEX][lex_rtree_t] Building scanner with flex 2.5.35 [ 1%] [BISON][parse_utree_t] Building parser with bison 2.4.1 [ 2%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/binary_io_operations.c.o [ 3%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/opt_algorithms.c.o [ 4%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_callback.c.o [ 5%] [FLEX][lex_utree_t] Building scanner with flex 2.5.35 [ 6%] [BISON][parse_rtree_t] Building parser with bison 2.4.1 Scanning dependencies of target pll_obj [ 6%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/pll_binary.c.o [ 6%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o [ 7%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_search.c.o [ 8%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir//pllmod_common.c.o [ 8%] Built target pllmodbinary_obj Scanning dependencies of target pllmodmsa_obj [ 9%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/pll_msa.c.o [ 10%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/pll_optimize.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 [ 11%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir//pllmod_common.c.o [ 11%] Built target pllmodmsa_obj [ 12%] [FLEX][lex_split_t] Building scanner with flex 2.5.35 [ 13%] [BISON][split_utree_t] Building 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[ 99%] Building CXX object src/CMakeFiles/raxml_module.dir/topology/RFDistCalculator.cpp.o [100%] Linking CXX shared module ../../bin/raxml-ng-mpi.so [100%] Built target raxml_module

Installing raxml-ng executable ...

-- Compiler: GNU 5.4.0 => /share/apps/gcc/5.4.0/bin/g++ -- Building RELEASE -- Using flags: -std=c++11 -Wall -Wextra -D_RAXML_PTHREADS -pthread -- Building dependencies in: /home/tdnavarrom/ParGenes/raxml-ng/build/localdeps -- pll-modules static build enabled -- 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;pll_static -- 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 -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY) -- GTest not found CMake Warning at test/src/CMakeLists.txt:5 (message): Skipping building tests.

-- Configuring done -- Generating done -- Build files have been written to: /home/tdnavarrom/ParGenes/raxml-ng/build -- Compiler: GNU 5.4.0 => /share/apps/gcc/5.4.0/bin/g++ -- Building RELEASE -- Using flags: -std=c++11 -Wall -Wextra -D_RAXML_PTHREADS -pthread -- Building dependencies in: /home/tdnavarrom/ParGenes/raxml-ng/build/localdeps -- pll-modules static build enabled -- 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;pll_static;pll_static -- 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 -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY) -- GTest not found CMake Warning at test/src/CMakeLists.txt:5 (message): Skipping building tests.

-- Configuring done -- Generating done -- Build files have been written to: /home/tdnavarrom/ParGenes/raxml-ng/build [ 3%] Built target pllmodbinary_obj [ 9%] Built target pllmodalgorithm_obj [ 11%] Built target pllmodoptimize_obj [ 41%] Built target pllmodmsa_obj [ 58%] Built target pll_obj [ 58%] Built target pllmodutil_obj [ 63%] Built target pllmodtree_obj [ 64%] Built target pll_static [ 65%] Built target pllmodoptimize_static [ 68%] Built target pllmodbinary_static [ 68%] Built target pllmodalgorithm_static [ 68%] Built target pllmodmsa_static [ 70%] Built target pllmodtree_static [ 70%] Built target pllmodutil_static Scanning dependencies of target raxml_module [ 70%] Building CXX object src/CMakeFiles/raxml_module.dir/AncestralStates.cpp.o [ 71%] Building CXX object src/CMakeFiles/raxml_module.dir/Checkpoint.cpp.o [ 73%] Building CXX object src/CMakeFiles/raxml_module.dir/CommandLineParser.cpp.o [ 73%] Building CXX object src/CMakeFiles/raxml_module.dir/ICScoreCalculator.cpp.o [ 73%] Building CXX object src/CMakeFiles/raxml_module.dir/MSA.cpp.o [ 74%] Building CXX object src/CMakeFiles/raxml_module.dir/Model.cpp.o [ 75%] Building CXX object src/CMakeFiles/raxml_module.dir/Optimizer.cpp.o [ 76%] Building CXX object src/CMakeFiles/raxml_module.dir/Options.cpp.o [ 76%] Building CXX object src/CMakeFiles/raxml_module.dir/ParallelContext.cpp.o [ 77%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionInfo.cpp.o [ 78%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionedMSA.cpp.o [ 79%] Building CXX object src/CMakeFiles/raxml_module.dir/PartitionedMSAView.cpp.o [ 80%] Building CXX object src/CMakeFiles/raxml_module.dir/SystemTimer.cpp.o [ 80%] Building CXX object src/CMakeFiles/raxml_module.dir/Tree.cpp.o [ 81%] Building CXX object src/CMakeFiles/raxml_module.dir/TreeInfo.cpp.o [ 82%] Building CXX object src/CMakeFiles/raxml_module.dir/log.cpp.o [ 83%] Building CXX object src/CMakeFiles/raxml_module.dir/main.cpp.o [ 83%] Building CXX object src/CMakeFiles/raxml_module.dir/util/SafetyCheck.cpp.o [ 84%] Building CXX object src/CMakeFiles/raxml_module.dir/util/parseutil.cpp.o [ 85%] Building CXX object src/CMakeFiles/raxml_module.dir/util/sysutil.cpp.o [ 86%] Building CXX object src/CMakeFiles/raxml_module.dir/io/NewickStream.cpp.o [ 86%] Building CXX object src/CMakeFiles/raxml_module.dir/io/RBAStream.cpp.o [ 87%] Building CXX object src/CMakeFiles/raxml_module.dir/io/ancestral_io.cpp.o [ 88%] Building CXX object src/CMakeFiles/raxml_module.dir/io/binary_io.cpp.o [ 89%] Building CXX object src/CMakeFiles/raxml_module.dir/io/msa_streams.cpp.o [ 90%] Building CXX object src/CMakeFiles/raxml_module.dir/io/part_info.cpp.o [ 90%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstopCheck.cpp.o [ 91%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstrapGenerator.cpp.o [ 92%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/BootstrapTree.cpp.o [ 93%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/ConsensusTree.cpp.o [ 93%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/SupportTree.cpp.o [ 94%] Building CXX object src/CMakeFiles/raxml_module.dir/bootstrap/TransferBootstrapTree.cpp.o [ 95%] Building CXX object src/CMakeFiles/raxml_module.dir/autotune/ResourceEstimator.cpp.o [ 96%] Building CXX object src/CMakeFiles/raxml_module.dir/loadbalance/BenoitLoadBalancer.cpp.o [ 96%] Building CXX object src/CMakeFiles/raxml_module.dir/loadbalance/KassianLoadBalancer.cpp.o [ 97%] Building CXX object src/CMakeFiles/raxml_module.dir/loadbalance/LoadBalancer.cpp.o [ 98%] Building CXX object src/CMakeFiles/raxml_module.dir/loadbalance/PartitionAssignment.cpp.o [ 99%] Building CXX object src/CMakeFiles/raxml_module.dir/topology/RFDistCalculator.cpp.o [100%] Linking CXX executable ../../bin/raxml-ng [100%] Built target raxml_module

Installing model-test-ng library ...

-- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- Check for working C compiler: /share/apps/gcc/5.4.0/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- Check for working CXX compiler: /share/apps/gcc/5.4.0/bin/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compier: GNU -- Building DEBUG -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Using flags: -std=c++11 -Wall -Wextra -DPTHREADS -pthread -D_NOGUI -D_MODELTEST_BUILD_AS_LIB -fPIC -- Building dependencies in: /home/tdnavarrom/ParGenes/modeltest/build/localdeps -- pll-modules static build enabled -- Found BISON: /usr/bin/bison (found version "2.4.1") -- Found FLEX: /usr/bin/flex (found version "2.5.35") -- 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 -- 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: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- Found MPI_CXX: /share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpicxx.so;/share/apps/mpich2/3.2/gcc-5.4.0/lib/libmpi.so
-- Modeltest will be built as a library. -- Configuring done -- Generating done -- Build files have been written to: /home/tdnavarrom/ParGenes/modeltest/build Scanning dependencies of target pllmodbinary_obj Scanning dependencies of target pllmodoptimize_obj Scanning dependencies of target pllmodalgorithm_obj [ 1%] [FLEX][lex_rtree_t] Building scanner with flex 2.5.35 [ 2%] [BISON][parse_utree_t] Building parser with bison 2.4.1 [ 3%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/binary_io_operations.c.o [ 4%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/opt_algorithms.c.o [ 5%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_callback.c.o [ 6%] [FLEX][lex_utree_t] Building scanner with flex 2.5.35 [ 6%] [BISON][parse_rtree_t] Building parser with bison 2.4.1 Scanning dependencies of target pll_obj [ 7%] Building C object 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13%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir//pllmod_common.c.o [ 14%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/lbfgsb.c.o [ 15%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linesearch.c.o [ 16%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o [ 17%] [FLEX][lex_split_t] Building scanner with flex 2.5.35 [ 17%] Built target pllmodalgorithm_obj [ 18%] [BISON][split_utree_t] Building parser with bison 2.4.1 [ 18%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o [ 19%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linpack.c.o Scanning dependencies of target pllmodtree_obj [ 20%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/consensus.c.o [ 21%] Building C object 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Built target pllmodutil_static [ 75%] Built target pllmodtree_static Scanning dependencies of target modeltest_module [ 75%] Building CXX object src/CMakeFiles/modeltest_module.dir/main.cpp.o [ 76%] Building CXX object src/CMakeFiles/modeltest_module.dir/meta.cpp.o [ 78%] Building CXX object src/CMakeFiles/modeltest_module.dir/modeltest.cpp.o [ 78%] Building CXX object src/CMakeFiles/modeltest_module.dir/model_selection.cpp.o [ 79%] Building CXX object src/CMakeFiles/modeltest_module.dir/msapll.cpp.o [ 79%] Building CXX object src/CMakeFiles/modeltest_module.dir/partition.cpp.o [ 80%] Building CXX object src/CMakeFiles/modeltest_module.dir/partition_selection.cpp.o [ 81%] Building CXX object src/CMakeFiles/modeltest_module.dir/partitioning_scheme.cpp.o [ 82%] Building CXX object src/CMakeFiles/modeltest_module.dir/static_analyzer.cpp.o [ 83%] Building CXX object src/CMakeFiles/modeltest_module.dir/treepll.cpp.o [ 84%] Building CXX object src/CMakeFiles/modeltest_module.dir/utils.cpp.o 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(base) [tdnavarrom@apolo ParGenes]$

`

tdnavarrom commented 5 years ago

After re-reinstalling ParGenes, and re-running the example, It started to work. I am going to close the issue, but it is weird how ParGenes started to work overnight.

Thanks