I am trying to build a Docker container based on the master branch, but I cannot get a clean compile and test run without errors. So far I've tried Ubuntu 24.04, 22.04 and Rocky Linux (Centos) 8.7 with no success. It seems this code is very sensitive to its build environment and I would like to be able to reproduce that environment as closely as possible.
Thanks much.
I see error messages such as this one generated when building with Ubuntu 22.04 (gcc 11.4.0):
`[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o
In file included from /REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8,
from /REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:2:
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const':
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:535:54: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'long unsigned int' [-Wformat=]
535
printf("bit array of size %lli: \n",_size);
~^ ~~~
long unsigned int
long long int
%li
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:539:54: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
539
printf(" (%llu) ",ii);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:52: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'long unsigned int' [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^
long long int
%li
In file included from /REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8,
from /REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:2:
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const':
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:535:54: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'long unsigned int' [-Wformat=]
535
printf("bit array of size %lli: \n",_size);
~^ ~~~
long unsigned int
long long int
%li
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:539:54: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
539
printf(" (%llu) ",ii);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:52: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'long unsigned int' [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^
long long int
%li
In file included from /REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8,
from /REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_64.cpp:2:
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const':
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:535:54: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'long unsigned int' [-Wformat=]
535
printf("bit array of size %lli: \n",_size);
~^ ~~~
long unsigned int
long long int
%li
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:539:54: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
539
printf(" (%llu) ",ii);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:52: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'long unsigned int' [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^
long long int
%li
In file included from /REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:8,
from /REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_96.cpp:2:
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In member function 'void boomphf::bitVector::print() const':
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:535:54: warning: format '%lli' expects argument of type 'long long int', but argument 2 has type 'long unsigned int' [-Wformat=]
535
printf("bit array of size %lli: \n",_size);
~^ ~~~
long unsigned int
long long int
%li
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:539:54: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
539
printf(" (%llu) ",ii);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^ ~~
uint64_t {aka long unsigned int}
long long unsigned int
%lu
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:548:52: warning: format '%lli' expects argument of type 'long long int', but argument 3 has type 'long unsigned int' [-Wformat=]
548
printf("%llu : %lli, ",ii,_ranks[ii]);
~~~^
long long int
%li
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf<elem_t, Hasher_t>::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]':
/REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:812:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::string, int, int, int, bool, bool) [with long unsigned int SPAN = 128; std::string = std::__cxx11::basic_string]'
/REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_128.cpp:30:9: required from here
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:839:50: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
839
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h: In instantiation of 'uint64_t boomphf::mphf<elem_t, Hasher_t>::totalBitSize() [with elem_t = long unsigned int; Hasher_t = gatb::core::debruijn::impl::hasher_t; uint64_t = long unsigned int]':
/REINDEER/bcalm2/gatb-core/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:812:60: required from 'void gatb::core::debruijn::impl::bglue(gatb::core::tools::storage::impl::Storage*, std::string, int, int, int, bool, bool) [with long unsigned int SPAN = 32; std::string = std::__cxx11::basic_string]'
/REINDEER/bcalm2/build/ext/gatb-core/src/gatb/template/TemplateSpecialization10.cpp.in_32.cpp:30:9: required from here
/REINDEER/bcalm2/build/ext/gatb-core/include/BooPHF/BooPHF.h:839:50: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=]
839
What is your standard development environment?
I am trying to build a Docker container based on the master branch, but I cannot get a clean compile and test run without errors. So far I've tried Ubuntu 24.04, 22.04 and Rocky Linux (Centos) 8.7 with no success. It seems this code is very sensitive to its build environment and I would like to be able to reproduce that environment as closely as possible.
Thanks much.
I see error messages such as this one generated when building with Ubuntu 22.04 (gcc 11.4.0):
~^ ~~~~^ ~~~~^ ~~~~^ ~~~~^~~~~^~~~c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[2]: [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/build.make:146: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... `
I get a different set of errors with Rocky Linux 8.7 (gcc 8.5.0):
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/build.make:132: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o] Error 1 make[2]: *** Waiting for unfinished jobs.... c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/build.make:174: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_96.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:296: ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2 make: *** [Makefile:156: all] Error 2 mv: cannot stat 'bcalm2/build/bcalm': No such file or directory echo "#define VERSION \"1.4.6.rc1-3-g59cdfe2\"" > version.h g++ -o blight.o -c blight/blight.cpp -DNDEBUG -Ofast -flto -msse4 -fstrict-aliasing -g -g -std=c++17 -pipe -lz -fopenmp -Iblight/lz4