CMAKE Shortestpath error for shared declaration #32

piyuveng1 · 2023-04-06T02:15:06Z

My process d getting stuck here don't know how to fix this. Please this help would be greatly appreciated!

$ make install
-- Configuring done
-- Generating done
-- Build files have been written to: /home/pv197/tn93/tn93
[ 10%] Built target tn93
[ 21%] Built target tn93-cluster
[ 31%] Built target seqcoverage
[ 34%] Building CXX object CMakeFiles/ShortestPathTN93.dir/src/ShortestPathTN93.cpp.o
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp: In function ‘void relaxDistanceEstimates(long unsigned int, long int, char, long int, double)’:
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘left_to_do’ is predetermined ‘shared’ for ‘shared’
#pragma omp parallel for default(none) shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates, step_penalty, min_overlap, resolutionOption, firstSequenceLength, theSequence, left_to_do)
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘theSequence’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘firstSequenceLength’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘resolutionOption’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘min_overlap’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘step_penalty’ is predetermined ‘shared’ for ‘shared’
make[2]: *** [CMakeFiles/ShortestPathTN93.dir/src/ShortestPathTN93.cpp.o] Error 1
make[1]: *** [CMakeFiles/ShortestPathTN93.dir/all] Error 2
make: *** [all] Error 2

piyuveng1 · 2023-04-06T02:18:18Z

add_executable(
ShortestPathTN93
src/ShortestPathTN93.cpp
src/stringBuffer.cc
src/tn93_shared.cc
)

add_executable(
selectreads
src/trim_reads.cpp
src/stringBuffer.cc
src/tn93_shared.cc
src/argparse_trim.cpp
)

add_executable(
validate_fasta
src/validate_fasta.cpp
src/stringBuffer.cc
src/tn93_shared.cc
)

add_executable(
fasta_diff
src/fasta_diff.cpp
src/stringBuffer.cc
src/tn93_shared.cc
src/argparse_fasta_diff.cpp
)

if(${OPENMP_FOUND})
add_definitions(${OpenMP_CXX_FLAGS})
target_link_libraries(tn93 PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(tn93-cluster PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(selectreads PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(seqcoverage PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(readreduce PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(fasta_diff PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(ShortestPathTN93 PUBLIC ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
target_link_libraries(seqdiff PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
endif(${OPENMP_FOUND})

install(
TARGETS ShortestPathTN93
RUNTIME DESTINATION bin
OPTIONAL
)

add_custom_target(TN93SP
DEPENDS ShortestPathTN93
)

install(
TARGETS nucfreqsfasta
RUNTIME DESTINATION bin
OPTIONAL
)

add_custom_target(NF
DEPENDS nucfreqsfasta
)

piyuveng1 · 2023-04-06T02:18:55Z

my cmakelist.txt with shortestpath references only

piyuveng1 · 2023-04-06T02:19:33Z

i dont see a shared error conflict if you can see it help me fix this! Please!

stevenweaver · 2023-04-06T15:00:23Z

Dear @piyuveng1,

Which compiler and platform are you using?

Best,
Steven

piyuveng1 · 2023-04-07T15:44:09Z

Dear @piyuveng1,

Which compiler and platform are you using?

Best, Steven

REDhat

stevenweaver · 2023-04-07T16:46:24Z

Dear @piyuveng1,

Can you please provide the output of gcc --version

Best,
Steven

piyuveng1 · 2023-04-10T01:11:44Z

gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)

stevenweaver · 2023-04-10T16:06:28Z

Dear @piyuveng1,

That gcc is really old (4.8 was released over 10 years ago). I'm surprised you are even able to compile since tn93 expects c++14 extensions. Would it be possible to use a later version of gcc via redhat toolset?

Best,
Steven

piyuveng1 · 2023-04-10T21:05:44Z

[pv197@ip-172-22-160-154 tn93]$ gcc --version
gcc (GCC) 7.3.1 20180303 (Red Hat 7.3.1-5)
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

/home/pv197/tn93/src/ShortestPathTN93.cpp: In function ‘void relaxDistanceEstimates(long unsigned int, long int, char, long int, double)’:
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘step_penalty’ is predetermined ‘shared’ for ‘shared’
#pragma omp parallel for default(none) shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates, step_penalty, min_overlap, resolutionOption, firstSequenceLength, theSequence, left_to_do)
^
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘min_overlap’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘resolutionOption’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘firstSequenceLength’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘theSequence’ is predetermined ‘shared’ for ‘shared’
/home/pv197/tn93/src/ShortestPathTN93.cpp:92:208: error: ‘left_to_do’ is predetermined ‘shared’ for ‘shared’
make[2]: *** [CMakeFiles/ShortestPathTN93.dir/build.make:83: CMakeFiles/ShortestPathTN93.dir/src/ShortestPathTN93.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:224: CMakeFiles/ShortestPathTN93.dir/all] Error 2
make: *** [Makefile:150: all] Error 2

Dear @ stevenweaver,

Thank u for taking the time i updated my gcc but still getting the same error.

ArtPoon · 2023-04-10T21:07:46Z

did you do a make clean first?

piyuveng1 · 2023-04-18T14:49:35Z

yes i did and now it's working thank you all!

…

On Mon, Apr 10, 2023 at 5:07 PM Art Poon ***@***.***> wrote: did you do a make clean first? — Reply to this email directly, view it on GitHub <#32 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABFUJDA3CR24DRKUGQR5YJDXARZCZANCNFSM6AAAAAAWUZYBXQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

niemasd · 2023-11-13T19:14:20Z

I'm getting this error using GCC 8.5 on Oracle Linux 8:

[root@codespaces-c478a0 tn93]# make clean
[root@codespaces-c478a0 tn93]# cmake .
-- Configuring done
-- Generating done
-- Build files have been written to: /workspaces/tn93
[root@codespaces-c478a0 tn93]# make
[  2%] Building CXX object CMakeFiles/nucfreqsfasta.dir/src/nuc_freqs_from_fasta.cpp.o
[  4%] Building CXX object CMakeFiles/nucfreqsfasta.dir/src/stringBuffer.cc.o
[  6%] Building CXX object CMakeFiles/nucfreqsfasta.dir/src/tn93_shared.cc.o
[  8%] Linking CXX executable nucfreqsfasta
[  8%] Built target nucfreqsfasta
[ 10%] Building CXX object CMakeFiles/readreduce.dir/src/read_reducer.cpp.o
/workspaces/tn93/src/read_reducer.cpp: In function ‘void handle_a_sequence(StringBuffer&, StringBuffer&, Vector&, Vector&, long int, long int, Vector*)’:
/workspaces/tn93/src/read_reducer.cpp:128:187: error: ‘firstSequenceLength’ is predetermined ‘shared’ for ‘shared’
             #pragma omp parallel for default(none) shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters, firstSequenceLength, min_overlap)
                                                                                                                                                                                           ^
/workspaces/tn93/src/read_reducer.cpp:128:187: error: ‘min_overlap’ is predetermined ‘shared’ for ‘shared’
make[2]: *** [CMakeFiles/readreduce.dir/build.make:76: CMakeFiles/readreduce.dir/src/read_reducer.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:129: CMakeFiles/readreduce.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
[root@codespaces-c478a0 tn93]# g++ --version
g++ (GCC) 8.5.0 20210514 (Red Hat 8.5.0-18.0.6)

niemasd · 2023-11-13T19:28:30Z

The issue I'm running into seems to be in more recent versions of GCC and/or OpenMP. Specifically, it seems like const variables shouldn't be specified in shared(...) clauses based on a Google search. I was able to get past this issue by making the following edits to the tn93 source code:

https://github.com/niemasd/tn93/blob/a00a7c830f71c31b35043d53cddc3e9e0ccf9878/Dockerfile#L7-L8

niemasd · 2023-11-13T19:29:54Z

I was able to fix the issue by making the following edits to the tn93 source:

sed -i 's/shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters, firstSequenceLength, min_overlap)/shared(currently_defined_clusters, try_cluster, sequence_lengths, current_sequence, current_clusters)/g' src/read_reducer.cpp
sed -i 's/shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates, step_penalty, min_overlap, resolutionOption, firstSequenceLength, theSequence, left_to_do)/shared(my_distance_estimate,nodeParents,workingNodes,distanceEstimates)/g' src/ShortestPathTN93.cpp

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

CMAKE Shortestpath error for shared declaration #32

CMAKE Shortestpath error for shared declaration #32

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

stevenweaver commented Apr 6, 2023

piyuveng1 commented Apr 7, 2023

stevenweaver commented Apr 7, 2023

piyuveng1 commented Apr 10, 2023

stevenweaver commented Apr 10, 2023

piyuveng1 commented Apr 10, 2023

ArtPoon commented Apr 10, 2023

piyuveng1 commented Apr 18, 2023 via email

niemasd commented Nov 13, 2023

niemasd commented Nov 13, 2023

niemasd commented Nov 13, 2023

CMAKE Shortestpath error for shared declaration #32

CMAKE Shortestpath error for shared declaration #32

Comments

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

piyuveng1 commented Apr 6, 2023

stevenweaver commented Apr 6, 2023

piyuveng1 commented Apr 7, 2023

stevenweaver commented Apr 7, 2023

piyuveng1 commented Apr 10, 2023

stevenweaver commented Apr 10, 2023

piyuveng1 commented Apr 10, 2023

ArtPoon commented Apr 10, 2023

piyuveng1 commented Apr 18, 2023 via email

niemasd commented Nov 13, 2023

niemasd commented Nov 13, 2023

niemasd commented Nov 13, 2023