SciDB (16.9) setup error


#1

I’m having a problem installing SciDB (16.9) on Ubuntu 14.04 machine.

I think I installed all the dependencies, but when I run “run.py setup”, I’m getting the following error message:

– Found Java: /usr/lib/jvm/java-1.8.0-openjdk-amd64/bin/java
– ****************** BEGIN src/storage/CMakeLists.txt ******************
– ****************** END src/storage/CMakeLists.txt ******************
– ****************** END src/CMakeLists.txt ******************
– copying /home/jiwon/workspace/SciDB/cdash to /home/jiwon/workspace/SciDB/stage/build/cdash
– copying /home/jiwon/workspace/SciDB/tests to /home/jiwon/workspace/SciDB/stage/build/tests
– removing /home/jiwon/workspace/SciDB/tests/harness/testcases/t from /home/jiwon/workspace/SciDB/stage/build/tests/harness/testcases/t
– ****************** END CMakeLists.txt ******************
– Configuring incomplete, errors occurred!
See also “/home/jiwon/workspace/SciDB/stage/build/CMakeFiles/CMakeOutput.log”.
See also “/home/jiwon/workspace/SciDB/stage/build/CMakeFiles/CMakeError.log”.
run.py: ERROR: Command setup failed: Abnormal return code: 1 on command [‘cmake’, ‘-DRUN_PY=1’, ‘-DCMAKE_BUILD_TYPE=Assert’, ‘-DCMAKE_INSTALL_PREFIX=/home/jiwon/workspace/SciDB/stage/install’, ‘/home/jiwon/workspace/SciDB’]
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests

and /home/jiwon/workspace/SciDB/stage/build/CMakeFiles/CMakeError.log contains the following error message:

Run Build Command:/usr/bin/make “cmTryCompileExec2092604934/fast”
/usr/bin/make -f CMakeFiles/cmTryCompileExec2092604934.dir/build.make CMakeFiles/cmTryCompileExec2092604934.dir/build
make[1]: Entering directory `/home/jiwon/workspace/SciDB/stage/build/CMakeFiles/CMakeTmp’
/usr/bin/cmake -E cmake_progress_report /home/jiwon/workspace/SciDB/stage/build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec2092604934.dir/CheckFunctionExists.c.o
/usr/bin/gcc-4.9 -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -fPIC -g -ggdb3 -fno-omit-frame-pointer -fPIC -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -Wconversion -Werror -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTryCompileExec2092604934.dir/CheckFunctionExists.c.o -c /usr/share/cmake-2.8/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2092604934
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2092604934.dir/link.txt --verbose=1
/usr/bin/gcc-4.9 -Wno-system-headers -isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_FORMAT_MACROS -D__STDC_LIMIT_MACROS -fPIC -g -ggdb3 -fno-omit-frame-pointer -fPIC -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-strict-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -Wconversion -Werror -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTryCompileExec2092604934.dir/CheckFunctionExists.c.o -o cmTryCompileExec2092604934 -rdynamic -lpthreads
/usr/bin/ld: cannot find -lpthreads

It seems like the error message could be misleading. I googled it and found out that cmake sometimes behaves wierd when some dependencies are missing. However, I installed all the dependency packages the setup process asked me to install.

What would be causing this?

thanks.


#2

Do you have the pthreads library installed?
/usr/lib/x86_64-linux-gnu/libpthread.a
/usr/lib/x86_64-linux-gnu/libpthread.so
ii libpthread-stubs0-dev:amd64 0.3-4 amd64 pthread stubs not provided by native libc, development files