Open nylander opened 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.
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
@kusalananda : Note that you need the file 20190115.nex
to run this example.
@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
Minor update: Running the same commands as above, but with a binary without beagle3 results in a hanging process (after a few 1000 generations).
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.
The same code on Ubuntu also shows no issues. I can't however test with GPU code...
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
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
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'
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.
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)
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
mb binary
mbblock.nex