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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
232 stars 79 forks source link

MPI issues: Heads up #100

Open nylander opened 5 years ago

nylander commented 5 years ago

Description:

Running mb.3.2.7 + beagle3 (GPU) crashes on Ubuntu 18.04. Trying to reproduce, and debug at the moment. More to come. Meanwhile:

Output

$ mpirun -np 9 /home/nylander/bin/mb.3.2.7-beagle3-mpi mbblock.nex 

[nylander-desk:07403] *** Process received signal ***
[nylander-desk:07403] Signal: Segmentation fault (11)
[nylander-desk:07403] Signal code: Address not mapped (1)
[nylander-desk:07403] Failing at address: 0x55f7c6ad031c
[nylander-desk:07403] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7fcdf8b43f20]
[nylander-desk:07403] [ 1] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x5d8fc)[0x55fa9676f8fc]
[nylander-desk:07403] [ 2] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x5fc98)[0x55fa96771c98]
[nylander-desk:07403] [ 3] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x75f1f)[0x55fa96787f1f]
[nylander-desk:07403] [ 4] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x9bcd8)[0x55fa967adcd8]
[nylander-desk:07403] [ 5] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x9fb0b)[0x55fa967b1b0b]
[nylander-desk:07403] [ 6] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x312e4)[0x55fa967432e4]
[nylander-desk:07403] [ 7] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x31eaa)[0x55fa96743eaa]
[nylander-desk:07403] [ 8] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x312e4)[0x55fa967432e4]
[nylander-desk:07403] [ 9] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x4403)[0x55fa96716403]
[nylander-desk:07403] [10] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x3e0c)[0x55fa96715e0c]
[nylander-desk:07403] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7fcdf8b26b97]
[nylander-desk:07403] [12] /home/nylander/bin/mb.3.2.7-beagle3-mpi(+0x3eaa)[0x55fa96715eaa]
[nylander-desk:07403] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 0 on node nylander-desk exited on signal 11 (Segmentation fault).

mb binary

$ ldd /home/nylander/bin/mb.3.2.7-beagle3-mpi
    linux-vdso.so.1 (0x00007fffa95f7000)
    libhmsbeagle.so.1 => /usr/local/lib/libhmsbeagle.so.1 (0x00007f4a30aa9000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4a3070b000)
    libmpi.so.20 => /usr/lib/x86_64-linux-gnu/libmpi.so.20 (0x00007f4a30419000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4a30028000)
    libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007f4a2fe1e000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f4a2fa95000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f4a2f87d000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f4a310ea000)
    libopen-rte.so.20 => /usr/lib/x86_64-linux-gnu/libopen-rte.so.20 (0x00007f4a2f5f5000)
    libopen-pal.so.20 => /usr/lib/x86_64-linux-gnu/libopen-pal.so.20 (0x00007f4a2f343000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f4a2f13b000)
    libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 (0x00007f4a2eefe000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4a2ecdf000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f4a2eadb000)
    libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f4a2e8d8000)
    libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00007f4a2e6cd000)

mbblock.nex

begin mrbayes;
    [MrBayes analysis of 20190115.nex. Wed 23 Jan 2019 03:32:50 PM CET: JN]
    [run with `mpirun -np 9 mb.3.2.7-beagle3-mpi mbblock.nex`]
    set autoclose=yes quitonerror=yes nowarnings=yes autoreplace=yes;
    set seed=1548256975 swapseed=1548256975;
    log start file=log.mb.20190115.log replace;
    exe 20190115.nex;
    charset Subset1 = 432-810\3 2-429\3 811-1564\3 431-810\3 1-429\3;
    charset Subset2 = 430-810\3 3-429\3 813-1564\3 1567-2157\3;
    charset Subset3 = 812-1564\3;
    charset Subset4 = 1565-2157\3;
    charset Subset5 = 1566-2157\3;
    partition PF = 5:Subset1, Subset2, Subset3, Subset4, Subset5;
    set partition=PF;
    lset applyto=(1) nst=6 rates=gamma;
    lset applyto=(2) nst=6 rates=gamma;
    lset applyto=(3) nst=6;
    lset applyto=(4) nst=2 rates=gamma;
    lset applyto=(5) nst=6 rates=gamma;
    prset applyto=(all) ratepr=variable;
    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);
    set usebeagle=yes beagledevice=CPU beagleprecision=single beaglescaling=dynamic;
    mcmcp mcmcdiagn=yes burninfrac=0.25 stoprule=yes stopval=0.01;
    mcmcp checkpoint=yes checkfreq=10000;
    mcmcp nruns=3 nchains=3 ngen=50000000;
    mcmc; [mcmc append=yes;]
    sump burninfrac=0.25 relburnin=yes hpd=yes;
    sumt burninfrac=0.25 relburnin=yes contype=allcompat conformat=simple calctreeprobs=yes showtreeprobs=no;
    log stop;
    quit;
end;
kusalananda commented 5 years ago

Could you post the output of mb -v (or Version interactively) so I can se exactly what compiler was used? Then I'll try to reproduce the issue in Docker.

nylander commented 5 years ago 
MrBayes > version

   ---------------------------------------------------------------------------

   Version

   MrBayes pre-3.2.7

   Features:  SSE AVX Beagle MPI
   Host type: x86_64-unknown-linux-gnu (CPU: x86_64)
   Compiler:  gnu 7.3.0
   ---------------------------------------------------------------------------

MrBayes > showb

   Available resources reported by beagle library:
    Resource 0:
    Name: CPU
    Flags: PROCESSOR_CPU PRECISION_DOUBLE PRECISION_SINGLE COMPUTATION_SYNCH
             EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO
             SCALING_ALWAYS SCALING_DYNAMIC SCALERS_RAW SCALERS_LOG
             VECTOR_NONE VECTOR_SSE THREADING_NONE THREADING_CPP

   BEAGLE version: 3.1.2 (PRE-RELEASE)

$ mpirun --version
mpirun (Open MPI) 2.1.1
nylander commented 5 years ago

@kusalananda : Note that you need the file 20190115.nex to run this example.

20190115.nex.gz

vivaxp5 commented 5 years ago

@kusalananda : Note that you need the file 20190115.nex (from me) to run this example. Dear Sir, I am facing the same issue. Could you kindly send me the nexus file. Mail ID: vivaxp5@gmail.com Anticipating your response.

Sincerely, Vivek

nylander commented 5 years ago

Minor update: Running the same commands as above, but with a binary without beagle3 results in a hanging process (after a few 1000 generations).

kusalananda commented 5 years ago

When running on macOS with

MrBayes, Bayesian Analysis of Phylogeny

Version:   3.2.7a
Features:  SSE AVX FMA Beagle MPI
Host type: x86_64-apple-darwin19.0.0 (CPU: x86_64)
Compiler:  clang 11.0.0

(current develop code), I have no issues after 20000 generations.

kusalananda commented 5 years ago

The same code on Ubuntu also shows no issues. I can't however test with GPU code...

vivaxp5 commented 5 years ago

When running on macOS with

MrBayes, Bayesian Analysis of Phylogeny

Version:   3.2.7a
Features:  SSE AVX FMA Beagle MPI
Host type: x86_64-apple-darwin19.0.0 (CPU: x86_64)
Compiler:  clang 11.0.0

(current develop code), I have no issues after 20000 generations.

Could you kindly guide me with the installation procedure from scratch? I have tried to set it up but to no avail.

Thanking you. Vivek

nylander commented 4 years ago

Dear @vivaxp5 ,

advice on installing can be found in the file [INSTALL] (https://github.com/NBISweden/MrBayes/blob/develop/INSTALL).

Please try it out and kindly inform us if you encounter any incorrect descriptions or bugs in the installation process related to the MrBayes code.

Cheers Johan

vivaxp5 commented 4 years ago

Dear Johan, I tried the installation using the current developer source code. I am getting errors while running the make command. PFA the complete log file appended for your reference.

List of errors is as follows - 1) best.c:1427:53: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] oldPLength=0.0, lambda=0.0, nu=0.0, igrvar=0.0, ^~ 2) proposal.c:4284:63: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] MrBFlt x, oldALength, oldCLength, extensionProb, nu, igrvar, rate, ^~ 3) proposal.c:7755:41: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] MrBFlt x, brlens, rate=NULL, igrvar=0.0, nu=0.0, oldALength, oldCLength; ^~ 4) proposal.c:8183:37: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] lambda=0.0, nu=0.0, igrvar=0.0, brlens=NULL, rate=NULL; ^~ 5) proposal.c:16228:39: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] brlens=NULL, nu=0.0, igrvar=0.0, *rate=NULL; ^~ 6) cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow]

Sincerely, Vivek

On Fri, Nov 15, 2019 at 7:51 PM Johan Nylander notifications@github.com wrote:

Dear @vivaxp5 https://github.com/vivaxp5 ,

advice on installing can be found in the file [INSTALL] ( https://github.com/NBISweden/MrBayes/blob/develop/INSTALL).

Please try it out and kindly inform us if you encounter any incorrect descriptions or bugs in the installation process related to the MrBayes code.

Cheers Johan

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/NBISweden/MrBayes/issues/100?email_source=notifications&email_token=AKVRMT25CAV4GAGMFCBPK33QT2V7JA5CNFSM4GTX7YU2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEFR7LA#issuecomment-554377132, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKVRMTYO4AKLHUEZ3QETMDDQT2V7JANCNFSM4GTX7YUQ .

-- Vivek Suranse, Evolutionary Venomics Lab: www.venomicslab.com TA-06. Centre for Ecological Sciences Indian Institute of Sciences. Bangalore 560012. Karnataka, India

kartik@kartik:/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop$ sudo ./configure --with-mpi [sudo] password for kartik: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for pdflatex... /usr/bin/pdflatex checking for bibtex... /usr/bin/bibtex checking for latexmk... /usr/bin/latexmk checking for style of include used by make... GNU checking whether to compile using MPI... yes checking for mpicc... mpicc checking for gcc... (cached) mpicc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether mpicc accepts -g... yes checking for mpicc option to accept ISO C89... none needed checking whether mpicc understands -c and -o together... yes checking dependency style of mpicc... gcc3 checking for function MPI_Init... yes checking for mpi.h... yes checking for sqrt in -lm... yes checking how to run the C preprocessor... mpicc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes configure: Trying to locate Beagle (hmsbeagle-1) in '/usr/local' checking libhmsbeagle/beagle.h usability... yes checking libhmsbeagle/beagle.h presence... yes checking for libhmsbeagle/beagle.h... yes checking for beagleCreateInstance in -lhmsbeagle... yes configure: Found Beagle in '/usr/local' checking for beagleSetCPUThreadCount in -lhmsbeagle... yes configure: Using BEAGLE_CFLAGS="-I/usr/local/include/libhmsbeagle-1 -pthread" configure: Using BEAGLE_LIBS="-L/usr/local/lib -Wl,-rpath,/usr/local/lib -lhmsbeagle" checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for memory.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for size_t... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for C compiler vendor... gnu checking for a sed that does not truncate output... /bin/sed checking for C compiler version... 7.4.0 checking CFLAGS for maximum warnings... -Wall checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 16:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 50654:65400800:7ffefbff:bfebfbff checking for x86 cpuid 0x00000007 output... 0:d39ffffb:18:9c002400 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 2ff:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C compiler accepts -madx... yes checking whether MPX is supported by the processor... yes checking whether MPX is supported by the processor and OS... yes checking whether C compiler accepts -mmpx... yes checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... yes checking whether AVX512-F is supported by the processor and OS... yes checking whether C compiler accepts -mavx512f... yes checking whether AVX512-CD is supported by the processor... yes checking whether AVX512-CD is supported by the processor and OS... yes checking whether C compiler accepts -mavx512cd... yes checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... yes checking whether AVX512-VL is supported by the processor and OS... yes checking whether C compiler accepts -mavx512vl... yes checking whether AVX512-BW is supported by the processor... yes checking whether AVX512-BW is supported by the processor and OS... yes checking whether C compiler accepts -mavx512bw... yes checking whether AVX512-DQ is supported by the processor... yes checking whether AVX512-DQ is supported by the processor and OS... yes checking whether C compiler accepts -mavx512dq... yes checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for strchr... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating doc/manual/Makefile config.status: creating doc/tutorial/Makefile config.status: creating doc/SMME_paper/Makefile config.status: creating examples/Makefile config.status: creating src/Makefile config.status: creating src/config.h config.status: executing depfiles commands kartik@kartik:/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop$ sudo make Making all in src make[1]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/src' make all-am make[2]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/src' mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-bayes.o -MD -MP -MF .deps/mb-bayes.Tpo -c -o mb-bayes.o test -f 'bayes.c' || echo './'bayes.c mv -f .deps/mb-bayes.Tpo .deps/mb-bayes.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-best.o -MD -MP -MF .deps/mb-best.Tpo -c -o mb-best.o test -f 'best.c' || echo './'best.c best.c: In function ‘Move_NodeSliderGeneTree’: best.c:1427:53: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] oldPLength=0.0, lambda=0.0, nu=0.0, igrvar=0.0, ^~ mv -f .deps/mb-best.Tpo .deps/mb-best.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-command.o -MD -MP -MF .deps/mb-command.Tpo -c -o mb-command.o test -f 'command.c' || echo './'command.c mv -f .deps/mb-command.Tpo .deps/mb-command.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-likelihood.o -MD -MP -MF .deps/mb-likelihood.Tpo -c -o mb-likelihood.o test -f 'likelihood.c' || echo './'likelihood.c mv -f .deps/mb-likelihood.Tpo .deps/mb-likelihood.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-mbbeagle.o -MD -MP -MF .deps/mb-mbbeagle.Tpo -c -o mb-mbbeagle.o test -f 'mbbeagle.c' || echo './'mbbeagle.c mv -f .deps/mb-mbbeagle.Tpo .deps/mb-mbbeagle.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-mcmc.o -MD -MP -MF .deps/mb-mcmc.Tpo -c -o mb-mcmc.o test -f 'mcmc.c' || echo './'mcmc.c mv -f .deps/mb-mcmc.Tpo .deps/mb-mcmc.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-model.o -MD -MP -MF .deps/mb-model.Tpo -c -o mb-model.o test -f 'model.c' || echo './'model.c mv -f .deps/mb-model.Tpo .deps/mb-model.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-proposal.o -MD -MP -MF .deps/mb-proposal.Tpo -c -o mb-proposal.o test -f 'proposal.c' || echo './'proposal.c proposal.c: In function ‘Move_ExtSSClock’: proposal.c:4284:63: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] MrBFlt x, oldALength, oldCLength, extensionProb, nu, igrvar, rate, ^~ proposal.c: In function ‘Move_NNIClock’: proposal.c:7755:41: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] MrBFlt x, brlens, rate=NULL, igrvar=0.0, nu=0.0, oldALength, oldCLength; ^~ proposal.c: In function ‘Move_NodeSliderClock’: proposal.c:8183:37: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] lambda=0.0, nu=0.0, igrvar=0.0, brlens=NULL, rate=NULL; ^~ proposal.c: In function ‘Move_TreeStretch’: proposal.c:16228:39: warning: variable ‘igrvar’ set but not used [-Wunused-but-set-variable] brlens=NULL, nu=0.0, igrvar=0.0, *rate=NULL; ^~ mv -f .deps/mb-proposal.Tpo .deps/mb-proposal.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-sumpt.o -MD -MP -MF .deps/mb-sumpt.Tpo -c -o mb-sumpt.o test -f 'sumpt.c' || echo './'sumpt.c mv -f .deps/mb-sumpt.Tpo .deps/mb-sumpt.Po mpicc -DHAVE_CONFIG_H -I. -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -MT mb-utils.o -MD -MP -MF .deps/mb-utils.Tpo -c -o mb-utils.o test -f 'utils.c' || echo './'utils.c utils.c: In function ‘ElTran’: cc1: warning: assuming signed overflow does not occur when assuming that (X - c) > X is always false [-Wstrict-overflow] mv -f .deps/mb-utils.Tpo .deps/mb-utils.Po mpicc -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -mrdrnd -mbmi -mbmi2 -madx -mmpx -mabm -I/usr/local/include/libhmsbeagle-1 -pthread -O3 -DNDEBUG -std=c99 -pedantic -Wall -o mb mb-bayes.o mb-best.o mb-command.o mb-likelihood.o mb-mbbeagle.o mb-mcmc.o mb-model.o mb-proposal.o mb-sumpt.o mb-utils.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lhmsbeagle -lm make[2]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/src' make[1]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/src' Making all in doc make[1]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc' Making all in manual make[2]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/manual' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/manual' Making all in SMME_paper make[2]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/SMME_paper' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/SMME_paper' Making all in tutorial make[2]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/tutorial' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc/tutorial' make[2]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc' make[1]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/doc' Making all in examples make[1]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/examples' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop/examples' make[1]: Entering directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/media/kartik/new/Bioinfo/Phylogenetics/Tree_building/MrBayes-develop'

kusalananda commented 4 years ago

Hi @vivaxp5

You will notice that none of those diagnostic messages constitutes an error. All of them are warnings and should not prevent the software from compiling.

pwkooij commented 1 year ago

Has there been any solution for this issue? I~m facing the same

mpirun -np 10 mb Leucocoprineae_species_20221122.nexus > log_restart6.txt &
[1] 46364

beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware
(If you have multiple ICDs installed and OpenCL works, you can ignore this message)
beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware
(If you have multiple ICDs installed and OpenCL works, you can ignore this message)
[atta:46373] *** Process received signal ***
[atta:46373] Signal: Segmentation fault (11)
[atta:46373] Signal code: Address not mapped (1)
[atta:46373] Failing at address: 0x24
[atta:46373] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f373f86c520]
[atta:46373] [ 1] mb(+0x8f441)[0x55b1e8474441]
[atta:46373] [ 2] mb(+0x8f920)[0x55b1e8474920]
[atta:46373] [ 3] mb(+0x9dee5)[0x55b1e8482ee5]
[atta:46373] [ 4] mb(+0x9e3af)[0x55b1e84833af]
[atta:46373] [ 5] mb(+0x31177)[0x55b1e8416177]
[atta:46373] [ 6] mb(+0x3187b)[0x55b1e841687b]
[atta:46373] [ 7] mb(+0x31177)[0x55b1e8416177]
[atta:46373] [ 8] mb(+0x5a4b)[0x55b1e83eaa4b]
[atta:46373] [ 9] mb(+0x545b)[0x55b1e83ea45b]
[atta:46373] [10] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f373f853d90]
[atta:46373] [11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f373f853e40]
[atta:46373] [12] mb(+0x54f5)[0x55b1e83ea4f5]
[atta:46373] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node atta exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
ldd /usr/local/bin/mb 
    linux-vdso.so.1 (0x00007ffc8c9c6000)
    libhmsbeagle.so.1 => /usr/local/lib/libhmsbeagle.so.1 (0x00007f63245f0000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f63244ef000)
    libmpi.so.40 => /lib/x86_64-linux-gnu/libmpi.so.40 (0x00007f63243b8000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6324190000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f6323f66000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f6323f44000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f6324836000)
    libopen-rte.so.40 => /lib/x86_64-linux-gnu/libopen-rte.so.40 (0x00007f6323e87000)
    libopen-pal.so.40 => /lib/x86_64-linux-gnu/libopen-pal.so.40 (0x00007f6323dd4000)
    libhwloc.so.15 => /lib/x86_64-linux-gnu/libhwloc.so.15 (0x00007f6323d78000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6323d5c000)
    libevent_core-2.1.so.7 => /lib/x86_64-linux-gnu/libevent_core-2.1.so.7 (0x00007f6323d25000)
    libevent_pthreads-2.1.so.7 => /lib/x86_64-linux-gnu/libevent_pthreads-2.1.so.7 (0x00007f6323d20000)
    libudev.so.1 => /lib/x86_64-linux-gnu/libudev.so.1 (0x00007f6323cf6000)