Closed kmeusemann closed 5 years ago
ArtPoon
commented
5 years ago Can you please provide some details about your system? e.g., run cat /proc/version if you're running Linux. I also suggest trying a slightly older release of HyPhy - you're using 2.4 alpha, which is pretty bleeding edge.
spond
commented
5 years ago Dear @kmeusemann,
That's a picky compiler you have there, but it found a real issue, which I just fixed in the develop branch. Try
git clone https://github.com/veg/hyphy.git hyphy-dev
cd hyphy-dev
git checkout develop
cmake ./
make installAs far as running multiple files, should be pretty straightforward via a shell script. How are your data formatted? Do you have a directory of alignments + trees?
Best, Sergei
kmeusemann
commented
5 years ago 1) ArtPoon: Linux version 4.4.0-142-generic (buildd@lgw01-amd64-033) (gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.10) ) #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 -> what version shall I use then?
2) @Sergej: ok i will try - and let you know how it goes! thanks :)) yes shell script but i have to figfure out exactly how etc - yes i have alignments & respective trees (and knowledge what i wanna take as forground - we aim to try relax (and maybe busted and/or aBSREL - not sure yet, but first i must get it to run and run e.g. 2 example files at all...
Best Karen
kmeusemann
commented
5 years ago Dear Sergej:
that worked thanks and looked good but I still get warnings about the HYPHYMP, HYPHYMPI etc. (see below). When i than after make install try again make MP or make MPI etc same errors as yesterday.
Does the command above automatically install MP or only HyPhy that can run on 1 thred (CPU) only? (aim would be to use MP / and or MPI so multiple threads)
sudo make install then also seemed to work... but see above. I am also wondering - can i call it somehow, is it then located in /usr/local/lib/hyphy I see no HYPHY executable in the folder i did cmake etc - so i again fail a bit.
when running the test script (I changed here HYPHYMP tp HYPHY is also gives me: ./run_unit_tests.sh ./tests/hbltests/UnitTests/HBLCommands/Abs.bf ./run_unit_tests.sh: line 16: /home/meusemann/Programs/HYPHY_dev/hyphy-dev/HYPHY: No such file or directory altough at the end it tells me :
also i find a lot here: /usr/local/lib/hyphy/ ChartAddIns GeneticCodes TemplateBatchFiles UserAddins data SubstitutionClasses TopologyInference DatapanelAddIns SubstitutionModels TreeAddIns b
but where is the executable then? (I also tried providing a prefix but that does not work either. sorry for bothering...
a step fw compared to yesterday, still i think not there yet...
best Karen
/home/meusemann/Programs/HYPHY_dev/hyphy-dev/run_tests.sh
-- Install configuration: "" -- Up-to-date: /usr/local/lib/hyphy -- Up-to-date: /usr/local/lib/hyphy
thanks & best Karen
cmake ./
-- The C compiler identification is GNU 5.4.0
-- The CXX compiler identification is GNU 5.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- 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: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Success
Set compiler flags to -fsigned-char -O3 -std=gnu++14 -march=corei7-avx -mtune=corei7-avx -g
-- 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
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.47.0")
-- Found PythonInterp: /usr/bin/python (found version "2.7.12")
-- 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
-- Found OpenCL: /usr/lib/x86_64-linux-gnu/libOpenCL.so
-- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so
-- Configuring done
WARNING: Target "HYPHYMP" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case.
WARNING: Target "HYPHYOCL" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case.
WARNING: Target "HYPHYMPI" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case.
-- Generating done
-- Build files have been written to: /home/meusemann/Programs/HYPHY_dev/hyphy-dev
spond
commented
5 years ago Dear @kmeusemann,
By default the binary goes to /usr/local/bin. You can try
$which HYPHYMPto see if the binary is in your path.
Best, Sergei
PS @rdvelazquez can you please follow up to make sure our installer/test scripts work out of the box as expected? They definitely should
kmeusemann
commented
5 years ago did it and its not in my PATH (also again checking with echo $PATH what its in my PATH, so it must have gone somewhere else - but not sure how to find out where.
when i specify a special place for the installation as described in the readme:
mkdir -p /opt/hyphy
`cmake -DINSTALL_PREFIX=/opt/hyphy .
that doesnot work: -> no executable is there. all additional files are however in /usr/local/lib/hyphy ...
maybe you can again write to install it locally specified, i can try again (make install does also not work either , works only with sudo, but then again - not in usr/local/bin neither user/bin etc pp...)
kmeusemann
commented
5 years ago quick note: i now try an older version, but here have again (but different) problems will try to solve it - hoping still for an solution for the current version. Aim is to run RELAX and BUSTED - I read now all tutorials wiki etc - but are there for example some EXAMPLE files how exactly the tree is labeled then (in Newick etc) (so input files - alignment / tree / batchfile examples for BUSTED/RELAXED) ?
Many thanks again Karen
kmeusemann
commented
5 years ago Hi, I finally made it to install properly HYPHY(MP), after solvinmg some other issues with libraries (connected with ld - so I have now executables: :) ! HYPHYMP (yeah...) but only for the previous version : hyphy-2.3.14/ appreciate if issues with the most current version are solved .
still looking for some example files for Busted/Relax - (trees and input batch files) - are they in tests or examples? Also - what is the difference between /RELAX-Groups.bf, RELAX.bf and RELAX-SRV.bf ?
Thanks again for all help! Karen
rdvelazquez
commented
5 years ago Hi @kmeusemann,
Thank you for letting us know about the issues. I hope my comments below are somewhat helpful:
Building HYPHYMP: Version 2.4.0-alpha is still under active development. It builds fine on the systems I'm able to test on but I will be working on improving the build system soon and the details of the issues you came across are helpful. Thanks again for sharing these! I'll reach out to you when I come across answers to your specific build questions.
Example Files:
./tests/hbltests/data/CD2.nex)Difference between RELAX batch files:
{anything_here}) in the newick tree. You are prompted to select which set of branches you want to use as the test set so the anything_here doesn't need to be a specific label. HyPhy also recognizes unlabeled branches (i.e. no curly brackets) as a set of branches so if you only have one set of labeled branches you can just use the "unlabeled branches" as the reference setRELAX-Groups.bf) but will be incorporated into the standard RELAX.bf batch file in version 2.4 onward.Additionally, I will note that we are working on providing standard command line invocation with keyword arguments for hyphy in version 2.4 which will make your batch analysis of thousands of files more straight forward than working around the interactive prompts. RELAX has yet to be ported over to use command line arguments but is next on my list. Busted should be good to go.
spond
commented
5 years ago Dear @kmeusemann,
Take a look at http://hyphy.org/tutorials/current-release-tutorial/#use-relax-to-compare-selective-pressures-on-different-parts-of-the-tree for a tutorial.
Best, Sergei
kmeusemann
commented
5 years ago Dear Ryan, Hi,
thansk so much for the feedback :)) some notes: 1) in the tutrorials http://hyphy.org/tutorials/phylotree/ there is that you for Busted need labeled branches: in case i wanna do with BUSTED on at least I aim to specify a set of foreground branches on which to test for positive selection (remaining branches are designated "background") - so here i need the branch labeled correct? - thanks for the links above :)
2) versions: for now I must stick to version 2.3.14 since 2.4. I am not able to get latter working. Anyway the option > 2 sets of branches in future versions will be great and I will push back to later since its i think useful and interesting :) (for first analyses i only have 2 sets of branches though).
3) working directly with command line will be invcredibly useful becaus alsthough it might be not too difficult to have this workaroubnd with creating batchfiles (that capture the interactive mode commands) for me is quite not that convenient - so I will hilghy appreciate this :+1: :-)
@spond : thasnks a lot again for the link! I missed that the alignment file includes the labeled tree at the bottom...
trying around with the batch file now (aim to analyse a lot genes for different species against all others species so quite a lot to analyse...
Many thanks again Karen
rdvelazquez
commented
5 years ago Hi @kmeusemann,
I'm currently checking to make sure our install/test scripts work as expected. Could you try a few things to help me pinpoint your exact issue?
git clone http://github.com/veg/hyphy hyphy-test-buildcd hyphy-test-buildgit checkout developcmake . (note the "dot" after cmake)make installAfter running through these steps could you:
which hyphyhyphy on your PATH (i.e. which hyphy does not return "no hyphy in..."), continue on, if not, see if there is an executable (hyphy) in the hyphy-test-build directory, if not run make hyphy and see if that creates an executable (hyphy) in the hyphy-test-build directoryhyphy-test-build directory.hyphy executable, try running hyphy slac --alignment <path_to_an_alignment_file> --tree <path_to_a_corresponding_tree_file> and see if that runs.Best, Ryan
relates to #930
kmeusemann
commented
5 years ago Dear Ryan,
since I am currently running a lot jobs, i probably will move testing to a later point when i have more time to do testing: short info: I have cmake 3.5.1 (in the readme it was as requirenment > 3.0 ... maybe that solved then already the issue, anyway i would liket to stick to the currently running version... gcc >= 4.9: gcc >= 4.9 libcurl: yes done libpthread: yes done openm: yes done
when i follow above still its installed in by path - and overwriting the now running version correct? so either i install it locally or i will come back when i have finished my other analyses - would that be ok? (or i try an additional computer).
many thanks Karen
rdvelazquez
commented
5 years ago Sounds good. No rush.
kmeusemann
commented
5 years ago short question: do you mean with "openm" actually openmpi ? Best, Karen (I uninstalled now cmake from the rpositories, installing 3.14.1 - but its gives me a could of weired messages,,... hope my system will still work... fingers crossed :))
kmeusemann
commented
5 years ago Dear Ryan,
now trying what you wrote above: along with the step make install I got the next error:
meusemann@oekoxx:~/Programs/hyphy-test-build$ make install Scanning dependencies of target hyphy [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/_hyExecutionContext.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/alignment.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/associative_list.cpp.o [ 5%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllist.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistx_iterator.cpp.o [ 10%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl.cpp.o [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/avllistxl_iterator.cpp.o [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/baseobj.cpp.o [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan.cpp.o [ 15%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlan2.cpp.o [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanhelpers.cpp.o [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/batchlanruntime.cpp.o [ 20%] Building CXX object CMakeFiles/hyphy.dir/src/core/calcnode.cpp.o [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/category.cpp.o [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/constant.cpp.o [ 25%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset.cpp.o [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter.cpp.o [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/dataset_filter_numeric.cpp.o [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/fisher_exact.cpp.o [ 30%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula.cpp.o [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/formula_parsing_context.cpp.o [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/fstring.cpp.o [ 35%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_object_lists.cpp.o [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/global_things.cpp.o [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/hbl_env.cpp.o [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc.cpp.o [ 40%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp: In member function ‘_List _LikelihoodFunction::RecoverAncestralSequencesMarginal(long int, _Matrix&, const _List&, bool)’: /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:896:50: error: call of overloaded ‘_String(long int&, bool)’ is ambiguous _String codeBuffer (unitLength, false); ^ In file included from /home/meusemann/Programs/hyphy-test-build/src/core/include/parser.h:46:0, from /home/meusemann/Programs/hyphy-test-build/src/core/include/category.h:43, from /home/meusemann/Programs/hyphy-test-build/src/core/include/likefunc.h:44, from /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:44: /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char format = nil); ^ /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:900:59: error: call of overloaded ‘_String(long int, bool)’ is ambiguous (result) < new _String(siteCountunitLength,false); ^ In file included from /home/meusemann/Programs/hyphy-test-build/src/core/include/parser.h:46:0, from /home/meusemann/Programs/hyphy-test-build/src/core/include/category.h:43, from /home/meusemann/Programs/hyphy-test-build/src/core/include/likefunc.h:44, from /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:44: /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char *format = nil); ^ CMakeFiles/hyphy.dir/build.make:413: recipe for target 'CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o' failed make[2]: [CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o] Error 1 CMakeFiles/Makefile2:232: recipe for target 'CMakeFiles/hyphy.dir/all' failed make[1]: [CMakeFiles/hyphy.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2
running it with sudo it again failed. also i have no executable
note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char format = nil); ^ CMakeFiles/hyphy.dir/build.make:413: recipe for target 'CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o' failed make[2]: [CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o] Error 1 CMakeFiles/Makefile2:232: recipe for target 'CMakeFiles/hyphy.dir/all' failed make[1]: [CMakeFiles/hyphy.dir/all] Error 2 Makefile:129: recipe for target 'all' failed make: *** [all] Error 2
then I checked: there is no hyphy executable in the hyphy-test-build directory
again giving me the same error and no executable: make hyphy [ 0%] Building CXX object CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp: In member function ‘_List _LikelihoodFunction::RecoverAncestralSequencesMarginal(long int, _Matrix&, const _List&, bool)’: /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:896:50: error: call of overloaded ‘_String(long int&, bool)’ is ambiguous _String codeBuffer (unitLength, false); ^ In file included from /home/meusemann/Programs/hyphy-test-build/src/core/include/parser.h:46:0, from /home/meusemann/Programs/hyphy-test-build/src/core/include/category.h:43, from /home/meusemann/Programs/hyphy-test-build/src/core/include/likefunc.h:44, from /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:44: /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char format = nil); ^ /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:900:59: error: call of overloaded ‘_String(long int, bool)’ is ambiguous (result) < new _String(siteCountunitLength,false); ^ In file included from /home/meusemann/Programs/hyphy-test-build/src/core/include/parser.h:46:0, from /home/meusemann/Programs/hyphy-test-build/src/core/include/category.h:43, from /home/meusemann/Programs/hyphy-test-build/src/core/include/likefunc.h:44, from /home/meusemann/Programs/hyphy-test-build/src/core/likefunc2.cpp:44: /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/meusemann/Programs/hyphy-test-build/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char *format = nil); ^ CMakeFiles/hyphy.dir/build.make:413: recipe for target 'CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o' failed make[3]: [CMakeFiles/hyphy.dir/src/core/likefunc2.cpp.o] Error 1 CMakeFiles/Makefile2:232: recipe for target 'CMakeFiles/hyphy.dir/all' failed make[2]: [CMakeFiles/hyphy.dir/all] Error 2 CMakeFiles/Makefile2:244: recipe for target 'CMakeFiles/hyphy.dir/rule' failed make[1]: [CMakeFiles/hyphy.dir/rule] Error 2 Makefile:229: recipe for target 'hyphy' failed make: [hyphy] Error 2
the makefile attached here (compressed as zip).
I hope that unless all done this hyphy 2.3.14 still works, it does not give me anything now typing which hyphy - which it did beofore doing all this.. anyway i can obviously still call it globally -> HYPHYMP gives me then the interactive mode of the previously successfully installed hyphy version: $ HYPHYMP /HYPHY 2.3.14.20190314beta(MP) for Linux on x86_64\ Makefile.zip
rdvelazquez
commented
5 years ago Thanks for trying that out @kmeusemann! A few things:
do you mean with "openm" actually openmpi ?
That should have been "openmp". Sorry about that. I don't think this is causing your issue though.
HYPHYMP 2.3.14 should still work fine
I don't immediately know why hyphy 2.4.0 isn't building for you but now that you have gone through those steps and provided the info I should have everything I need to look into it further so thank you!
I'll get back to you once I locate the issue.
stevenweaver
commented
5 years ago Dear @rdvelazquez,
I would like to add that I also have the exact same error as @kmeusemann when trying to build develop using gcc 5.
Best, Steven
rdvelazquez
commented
5 years ago Thank you @stevenweaver. I don't have the issue when using aocc 1.2.1 on linux and AppleClang 10.0.0 on mac. I'll try to reproduce with gcc and troubleshoot.
rdvelazquez
commented
5 years ago @kmeusemann I can confirm that this issue occurs with gcc 5 but not with gcc 6... If you would like to use the develop branch and can get gcc 6 that may be the fastest way and the path with the least resistance.
@spond The issue that gcc 5 is having may have been introduced with:
See:
spond
commented
5 years ago Dear @rdvelazquez,
That's actually a real bug left over from refactoring -- I am fixing it in the next push.
Best, Sergei
kmeusemann
commented
5 years ago ok sounds good - (and glad that I am not the only one with that problem. Sergei/Ryan: ok then plan is to install gcc v6 and try again from ryan above? also if there are options to run it on command line directly (instead of generating files that catch interactively mode) are highly appreciated!
Best Karen
rdvelazquez
commented
5 years ago @kmeusemann just to provide an update:
HYPHYMP relax --help to see the arguments that you should provide. This is still in active development so you may see strange behavior and please reach out to us if you do.We'll let you know once the gcc v5 issue is resolved.
spond
commented
5 years ago Dear all,
The gcc5 issues should have been resolved with the current develop branch
Best, Sergei
kmeusemann
commented
5 years ago Dear Sergei & Ryan:
1) I successfully could compile now the 2.4.0alpha version form the developer bracnch using currently gcc gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.10) and cmake version 3.14.1 2) I reran the one analyses with RELAX that failed in version 2.3.14: it works now and the "main" result but several values are different , I post this to #930
Many thanks Karen
Hi,
I am new to Hyphy - and later need to run (either busted or relaxed) on several thousand files (thus non-interactively, command line etc which seems also to be a bit tricky and complex). Maybe stupid, but I fail already to generate a executable (I have version cmake 3.5.1, installed additionally
I get same errors no matter if I tray make MP, make MPI or make HYPHYMPI, make GTEST
I get warnings already doing cmake (path here replaced by KM):
cmake .
(I searched here and other platforms but cannot figure out the problem):
Set compiler flags to -fsigned-char -O3 -std=gnu++14 -march=corei7-avx -mtune=corei7-avx -g -- Configuring done WARNING: Target "HYPHYMP" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case. WARNING: Target "HYPHYOCL" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case. WARNING: Target "HYPHYMPI" has EXCLUDE_FROM_ALL set and will not be built by default but an install rule has been provided for it. CMake does not define behavior for this case. -- Generating done -- Build files have been written to: /home/KM/hyphy-2.4.0-alpha.1
What does it mean - do i have to change something somwhere? (CMakeLists / other files - I am not familiar with C++ though)
when i then still try to go on it also gives me errors I don't understand and don't know how to fix them. (probably caused by message above)..
HELP much appreciated! Many thanks Karen
/home/KM/hyphy-2.4.0-alpha.1$ make MP Scanning dependencies of target HYPHYMP [ 5%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlanhelpers.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/variable.cpp.o [ 5%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/constant.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlan.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/matrix.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistxl_iterator.cpp.o [ 10%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/string_file_wrapper.cpp.o [ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/polynoml.cpp.o [ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/global_object_lists.cpp.o [ 15%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/alignment.cpp.o [ 20%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/batchlan2.cpp.o [ 20%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/avllistx_iterator.cpp.o [ 20%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/category.cpp.o [ 25%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/parser2.cpp.o [ 25%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/tree_iterator.cpp.o [ 25%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/string_buffer.cpp.o [ 30%] Building CXX object CMakeFiles/HYPHYMP.dir/src/core/dataset_filter.cpp.o /home/KM/hyphy-2.4.0-alpha.1/src/core/dataset_filter.cpp: In member function ‘long unsigned int _DataSetFilter::FindUniqueSequences(_SimpleList&, _SimpleList&, _SimpleList&, short int) const’: /home/KM/hyphy-2.4.0-alpha.1/src/core/dataset_filter.cpp:170:43: error: call of overloaded ‘_String(long unsigned int&, bool)’ is ambiguous _String state1 (unit,false), ^ In file included from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/parser.h:46:0, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/translation_table.h:45, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/dataset.h:45, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/dataset_filter.h:44, from /home/KM/hyphy-2.4.0-alpha.1/src/core/dataset_filter.cpp:42: /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char format = nil); ^ /home/KM/hyphy-2.4.0-alpha.1/src/core/dataset_filter.cpp:171:27: error: call of overloaded ‘_String(long unsigned int&, bool)’ is ambiguous state2 (unit,false); ^ In file included from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/parser.h:46:0, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/translation_table.h:45, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/dataset.h:45, from /home/KM/hyphy-2.4.0-alpha.1/src/core/include/dataset_filter.h:44, from /home/KM/hyphy-2.4.0-alpha.1/src/core/dataset_filter.cpp:42: /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:243:3: note: candidate: _String::_String(const _String&, long unsigned int) _String(const _String &str, unsigned long copies); ^ /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:151:5: note: candidate: _String::_String(hyFloat, unsigned char) _String(const hyFloat number, unsigned char digits_of_precision); ^ /home/KM/hyphy-2.4.0-alpha.1/src/core/include/hy_strings.h:140:3: note: candidate: _String::_String(hyFloat, const char) _String(const hyFloat number, const char format = nil); ^ CMakeFiles/HYPHYMP.dir/build.make:446: recipe for target 'CMakeFiles/HYPHYMP.dir/src/core/dataset_filter.cpp.o' failed make[3]: [CMakeFiles/HYPHYMP.dir/src/core/dataset_filter.cpp.o] Error 1 CMakeFiles/Makefile2:227: recipe for target 'CMakeFiles/HYPHYMP.dir/all' failed make[2]: [CMakeFiles/HYPHYMP.dir/all] Error 2 CMakeFiles/Makefile2:170: recipe for target 'CMakeFiles/MP.dir/rule' failed make[1]: [CMakeFiles/MP.dir/rule] Error 2 Makefile:201: recipe for target 'MP' failed make: [MP] Error 2