Help build MPI version

[rdauria]

Hello,

I am trying to build MAPGD (version 0.4.38) on a system with IntelMPI (Version 2018 Update 4) and gcc (version 4.9.3). I get the following error:

mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope

In more details:

g++ -std=c++11 -g -O2 -DVERSION=\"0.4.39\"  -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi  -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\"  -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi  -I ./sql -c -o objs/system.o system/system.cc 
mpicxx -std=c++11 -g -O2 -DVERSION=\"0.4.39\"  -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi  -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\"  -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi  -I ./sql -c -o objs/mpi_relatedness.o mpi/mpi_relatedness.cc 
mpi/mpi_relatedness.cc: In function ‘int estimateRel(int, char**)’:
mpi/mpi_relatedness.cc:171:59: error: too few arguments to function ‘std::map<std::tuple<float, float, float, float, float, float, float>, long unsigned int> hash_genotypes(const stringstream&, const size_t&, const size_t&, const bool&, const bool&)’
     hashed_genotypes=hash_genotypes(file_buffer, x, y, l2o);
                                                           ^
In file included from mpi/mpi_relatedness.h:6:0,
                 from mpi/mpi_relatedness.cc:1:
./commands/relatedness.h:44:1: note: declared here
 hash_genotypes (const std::stringstream &, const size_t &, const size_t &, const bool &, const bool &);
 ^
mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope
         get_95CI(relatedness, hashed_genotypes);
                                               ^
make[2]: *** [objs/mpi_relatedness.o] Error 1
make[2]: Leaving directory `/home/test/MAPGD-master/src/mapgd_0.4'
make[1]: *** [mapgd_0.4] Error 2
make[1]: Leaving directory `/home/test/MAPGD-master/src'
make: *** [src] Error 2

Indeed get_95CI does not appear to be declared in mpi_relatedness.cc:

$  grep -R get_95CI *
IDRE_make.log:mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope
IDRE_make.log:         get_95CI(relatedness, hashed_genotypes);
src/mapgd_0.4/commands/relatedness.cc:get_95CI(Relatedness &rel, std::map <Genotype_pair_tuple, size_t> hashed_genotypes)
src/mapgd_0.4/commands/relatedness.cc:            if (relatedness.success_) get_95CI(relatedness, hashed_genotypes);
src/mapgd_0.4/mpi/mpi_relatedness.cc:				    get_95CI(relatedness, hashed_genotypes);
Binary file src/mapgd_0.4/objs/relatedness.o matches

Any idea?

Thanks!

RD

[matthew-ackerman]

I'll look into it and get back to you. The automated test are not running correctly right now, so I may have overlooked some problems.

…

On Mon, 29 Mar 2021, 4:38 pm rd, ***@***.***> wrote: Hello, I am trying to build MAPGD (version 0.4.38) on a system with IntelMPI (Version 2018 Update 4) and gcc (version 4.9.3). I get the following error: mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope In more details: g++ -std=c++11 -g -O2 -DVERSION=\"0.4.39\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\" -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -c -o objs/system.o system/system.cc mpicxx -std=c++11 -g -O2 -DVERSION=\"0.4.39\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\" -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -c -o objs/mpi_relatedness.o mpi/mpi_relatedness.cc mpi/mpi_relatedness.cc: In function ‘int estimateRel(int, char**)’: mpi/mpi_relatedness.cc:171:59: error: too few arguments to function ‘std::map<std::tuple<float, float, float, float, float, float, float>, long unsigned int> hash_genotypes(const stringstream&, const size_t&, const size_t&, const bool&, const bool&)’ hashed_genotypes=hash_genotypes(file_buffer, x, y, l2o); ^ In file included from mpi/mpi_relatedness.h:6:0, from mpi/mpi_relatedness.cc:1: ./commands/relatedness.h:44:1: note: declared here hash_genotypes (const std::stringstream &, const size_t &, const size_t &, const bool &, const bool &); ^ mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope get_95CI(relatedness, hashed_genotypes); ^ make[2]: *** [objs/mpi_relatedness.o] Error 1 make[2]: Leaving directory `/home/test/MAPGD-master/src/mapgd_0.4' make[1]: *** [mapgd_0.4] Error 2 make[1]: Leaving directory `/home/test/MAPGD-master/src' make: *** [src] Error 2 Indeed get_95CI does not appear to be declared in mpi_relatedness.cc: $ grep -R get_95CI * IDRE_make.log:mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope IDRE_make.log: get_95CI(relatedness, hashed_genotypes); src/mapgd_0.4/commands/relatedness.cc:get_95CI(Relatedness &rel, std::map <Genotype_pair_tuple, size_t> hashed_genotypes) src/mapgd_0.4/commands/relatedness.cc: if (relatedness.success_) get_95CI(relatedness, hashed_genotypes); src/mapgd_0.4/mpi/mpi_relatedness.cc: get_95CI(relatedness, hashed_genotypes); Binary file src/mapgd_0.4/objs/relatedness.o matches Any idea? Thanks! RD — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#38>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACRUFWINJBJ632W42QAPBDTGDXMXANCNFSM42APHBPA> .

[matthew-ackerman]

MPI should be working. it is only used for relatedness calculations, and please please be cautious with the output of mapgd relatedness. I suspect it is garbage right now, but I'm having trouble fixing it. If you really need that feature I suggest using an older version of mapgd. I can give you the specifics if neccisary.

…

-Matt On Tue, Mar 30, 2021 at 10:42 AM Matthew Ackerman < ***@***.***> wrote:

I'll look into it and get back to you. The automated test are not running correctly right now, so I may have overlooked some problems. On Mon, 29 Mar 2021, 4:38 pm rd, ***@***.***> wrote: > Hello, > > I am trying to build MAPGD (version 0.4.38) on a system with IntelMPI > (Version 2018 Update 4) and gcc (version 4.9.3). I get the following error: > > mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this > scope > > In more details: > > g++ -std=c++11 -g -O2 -DVERSION=\"0.4.39\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\" -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -c -o objs/system.o system/system.cc > > mpicxx -std=c++11 -g -O2 -DVERSION=\"0.4.39\" -Wno-write-strings -fno-exceptions -pedantic -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -fopenmp -DUSE_MAN -DDOCPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd\" -DMANPATH=\"/home/test/MAPGD/0.4.38/share/doc/mapgd/man\" -DPATH=\"/home/test/MAPGD/0.4.38/share/mapgd\" -DPWD=\"`pwd`\" -DNOHTS -DNOLZ4 -I ./ -I ./data_types/ -I ./commands/ -I ./raw/ -I ./data_conversion/ -I ./gzstream/ -I ./stream_tools/ -I ./io/ -I ./math_functions/ -I ./system/ -I ./mpi -I ./sql -c -o objs/mpi_relatedness.o mpi/mpi_relatedness.cc > > mpi/mpi_relatedness.cc: In function ‘int estimateRel(int, char**)’: > > mpi/mpi_relatedness.cc:171:59: error: too few arguments to function ‘std::map<std::tuple<float, float, float, float, float, float, float>, long unsigned int> hash_genotypes(const stringstream&, const size_t&, const size_t&, const bool&, const bool&)’ > > hashed_genotypes=hash_genotypes(file_buffer, x, y, l2o); > > ^ > > In file included from mpi/mpi_relatedness.h:6:0, > > from mpi/mpi_relatedness.cc:1: > > ./commands/relatedness.h:44:1: note: declared here > > hash_genotypes (const std::stringstream &, const size_t &, const size_t &, const bool &, const bool &); > > ^ > > mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope > > get_95CI(relatedness, hashed_genotypes); > > ^ > > make[2]: *** [objs/mpi_relatedness.o] Error 1 > > make[2]: Leaving directory `/home/test/MAPGD-master/src/mapgd_0.4' > > make[1]: *** [mapgd_0.4] Error 2 > > make[1]: Leaving directory `/home/test/MAPGD-master/src' > > make: *** [src] Error 2 > > > Indeed get_95CI does not appear to be declared in mpi_relatedness.cc: > > $ grep -R get_95CI * > > IDRE_make.log:mpi/mpi_relatedness.cc:178:47: error: ‘get_95CI’ was not declared in this scope > > IDRE_make.log: get_95CI(relatedness, hashed_genotypes); > > src/mapgd_0.4/commands/relatedness.cc:get_95CI(Relatedness &rel, std::map <Genotype_pair_tuple, size_t> hashed_genotypes) > > src/mapgd_0.4/commands/relatedness.cc: if (relatedness.success_) get_95CI(relatedness, hashed_genotypes); > > src/mapgd_0.4/mpi/mpi_relatedness.cc: get_95CI(relatedness, hashed_genotypes); > > Binary file src/mapgd_0.4/objs/relatedness.o matches > > > Any idea? > > Thanks! > > RD > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#38>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AACRUFWINJBJ632W42QAPBDTGDXMXANCNFSM42APHBPA> > . >

[rdauria]

Thanks for taking care of this issue. I am now able to build the code.

Regards,

RD