Error occurred on upgrading 14.x SciDB to 15.x


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/opt/rh/devtoolset-3/root/usr/bin/g++    -std=c++14 -pedantic -W -Wextra -Wall -Wno-unused-local-typedefs -Wno-stric-aliasing -Wno-long-long -Wno-unused-parameter -Wno-variadic-macros -fPIC -D__STDC_FORMAT_MACROS -Wno-system-headers-isystem /opt/local/include/ -isystem /usr/local/include/ -D__STDC_LIMIT_MACROS -DPROJECT_ROOT=\"/home/scidb/scidb-1.12.1.4cadab5/\" -Wconversion -g  -Wl,--enable-new-dtags CMakeFiles/scidb.dir/network/entry.cpp.o CMakeFiles/scidb.dr/network/GlobalNew.cpp.o CMakeFiles/scidb.dir/dense_linear_algebra/blas/initMathLibs.cpp.o  -o ../bin/scidb  -L/usrlocal/lib -rdynamic network/libnetwork_lib.a util/libutil_lib.a system/libsystem_lib.a query/libqproc_lib.a array/liarray_lib.a -lrt -lpthread -ldl /usr/local/lib64/libblas.a /usr/local/lib64/liblapack.a /usr/local/lib64/libblas.a /pt/scidb/15.12/3rdparty/cityhash/lib/libcityhash.so usr_namespace/libusr_namespace_lib.a smgr/io/libio_lib.a query/lbscalar_proc_lib.a query/ops/libops_lib.a network/libnetwork_lib.a query/libqproc_lib.a usr_namespace/libusr_namespae_lib.a smgr/io/libio_lib.a query/libscalar_proc_lib.a query/ops/libops_lib.a network/proto/libscidb_msg_lib.a -lproobuf array/libarray_lib.a system/catalog/libcatalog_lib.a -lpqxx -lpq util/libutil_lib.a -lrt smgr/compression/libcopression_lib.a system/libsystem_lib.a -lpthread /usr/local/lib/liblog4cxx.so ../extern/lib_json/libjson_lib.a /opt/sidb/15.12/3rdparty/boost/lib/libboost_system.so /opt/scidb/15.12/3rdparty/boost/lib/libboost_program_options.so /optscidb/15.12/3rdparty/boost/lib/libboost_serialization.so /opt/scidb/15.12/3rdparty/boost/lib/libboost_regex.so /opt/cidb/15.12/3rdparty/boost/lib/libboost_filesystem.so /opt/scidb/15.12/3rdparty/boost/lib/libboost_thread.so /opt/scib/15.12/3rdparty/boost/lib/libboost_date_time.so -lz -lbz2 -lcsv ../extern/MurmurHash/libMurmurHash_lib.a /usr/locallib64/liblapack.a /opt/scidb/15.12/3rdparty/cityhash/lib/libcityhash.so -Wl,-rpath,"\$ORIGIN/../plugins:\$ORIGIN/../ib:\$ORIGIN/../../:/usr/local/lib:/opt/scidb/15.12/3rdparty/cityhash/lib:/opt/scidb/15.12/3rdparty/boost/lib"
/usr/local/lib64/libblas.a(xerbla.f.o): In function `xerbla_':
xerbla.f:(.text+0x68): undefined reference to `_gfortran_st_write'
xerbla.f:(.text+0x7f): undefined reference to `_gfortran_string_len_trim'
xerbla.f:(.text+0xa2): undefined reference to `_gfortran_transfer_character'
xerbla.f:(.text+0xc0): undefined reference to `_gfortran_transfer_integer'
xerbla.f:(.text+0xcf): undefined reference to `_gfortran_st_write_done'
xerbla.f:(.text+0xd9): undefined reference to `_gfortran_stop_numeric'
/usr/local/lib64/liblapack.a(dormlq.f.o): In function `dormlq_':
dormlq.f:(.text+0x2d0): undefined reference to `_gfortran_concat_string'
dormlq.f:(.text+0x478): undefined reference to `_gfortran_concat_string'
/usr/local/lib64/liblapack.a(dormqr.f.o): In function `dormqr_':
dormqr.f:(.text+0x2c9): undefined reference to `_gfortran_concat_string'
dormqr.f:(.text+0x471): undefined reference to `_gfortran_concat_string'
/usr/local/lib64/liblapack.a(ilaenv.f.o): In function `ilaenv_':
ilaenv.f:(.text+0x3fe): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x421): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x45e): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x47d): undefined reference to `_gfortran_compare_string'
ilaenv.f:(.text+0x49c): undefined reference to `_gfortran_compare_string'
/usr/local/lib64/liblapack.a(ilaenv.f.o):ilaenv.f:(.text+0x4bb): more undefined references to `_gfortran_compare_strng' follow
collect2: error: ld returned 1 exit status
make[2]: *** [bin/scidb] 오류 1
make[1]: *** [src/CMakeFiles/scidb.dir/all] 오류 2
make: *** [all] 오류 2
run.py: ERROR: Command make failed: Abnormal return code: 2 on command ['/usr/bin/make', '-j1']
run.py: ERROR: Make sure commands setup,make,install,start are performed (in that order) before stop,stopForce,tests

Hey all, I bumped into these issues while trying to install SciDB 15.12 on CentOS 6.5
Anyone knows how to solve this?
Thanks, Mj Kim


#2

Hi,

It looks like you might be missing some fortran libraries. Did you try this:

$ cd deployment
$ sudo ./deploy.sh prepare_toolchain localhost