{"action":"opened","issue":{"url":"https://api.github.com/repos/GEOSX/thirdPartyLibs/issues/9","repository_url":"https://api.github.com/repos/GEOSX/thirdPartyLibs","labels_url":"https://api.github.com/repos/GEOSX/thirdPartyLibs/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/GEOSX/thirdPartyLibs/issues/9/comments","events_url":"https://api.github.com/repos/GEOSX/thirdPartyLibs/issues/9/events","html_url":"https://github.com/GEOSX/thirdPartyLibs/issues/9","id":349376301,"node_id":"MDU6SXNzdWUzNDkzNzYzMDE=","number":9,"title":"Error when building silo","user":{"login":"klevzoff","id":1550292,"node_id":"MDQ6VXNlcjE1NTAyOTI=","avatar_url":"https://avatars1.githubusercontent.com/u/1550292?v=4","gravatar_id":"","url":"https://api.github.com/users/klevzoff","html_url":"https://github.com/klevzoff","followers_url":"https://api.github.com/users/klevzoff/followers","following_url":"https://api.github.com/users/klevzoff/following{/other_user}","gists_url":"https://api.github.com/users/klevzoff/gists{/gist_id}","starred_url":"https://api.github.com/users/klevzoff/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/klevzoff/subscriptions","organizations_url":"https://api.github.com/users/klevzoff/orgs","repos_url":"https://api.github.com/users/klevzoff/repos","events_url":"https://api.github.com/users/klevzoff/events{/privacy}","received_events_url":"https://api.github.com/users/klevzoff/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-10T04:58:23Z","updated_at":"2018-08-10T04:58:23Z","closed_at":null,"author_association":"NONE","body":"System: Ubuntu 18.04, gcc-7.3.0 (reproduces on each of 3 Ubuntu systems I have, including a freshly installed one)\r\n\r\nWith some recent commits in `develop` (can't pinpoint the exact time, but seems some time during the last 2-3 weeks) I started getting the following error when building `silo`:\r\n```\r\nchecking for hdf5... configure: checking for hdf5 and supporting libraries...\r\nchecking hdf5.h usability... yes\r\nchecking hdf5.h presence... yes\r\nchecking for hdf5.h... yes\r\nchecking for H5open... no\r\nconfigure: checking if lack of zlib caused tests for hdf5 to fail...\r\nchecking hdf5.h usability... yes\r\nchecking hdf5.h presence... yes\r\nchecking for hdf5.h... yes\r\nchecking for H5open in -lhdf5... no\r\nconfigure: error:\r\nYou have made an explicit request for hdf5 with the --with-hdf option\r\nand ../silo/configure is unable to find hdf5 and its supporting libs, if any.\r\nPlease see INSTALL_FAQ for possible causes.\r\nCMakeFiles/silo.dir/build.make:108: recipe for target 'silo/src/silo-stamp/silo-configure' failed\r\nmake[3]: *** [silo/src/silo-stamp/silo-configure] Error 1\r\n```\r\nThe library `libhdf5.a` exists in the expected location (`../install-default-release/hdf5`) and does contain the function `H5open`.\r\n\r\n`config.log` says:\r\n```\r\nconfigure:29453: checking for H5open in -lhdf5\r\nconfigure:29496: /usr/bin/mpicc -o conftest -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -Wdeclaration-after-statement -I/home/klevtsov/work/geosx/thirdPartyLibs/install-default-release/hdf5/include  -L/home/klevtsov/work/geosx/thirdPartyLibs/install-default-release/hdf5/lib -ldl conftest.c -lhdf5  -lz  -lm >&5\r\n/usr/bin/x86_64-linux-gnu-ld: /home/klevtsov/work/geosx/thirdPartyLibs/install-default-release/hdf5/lib/libhdf5.a(H5PL.o): undefined reference to symbol 'dlclose@@GLIBC_2.2.5'\r\n/usr/lib/gcc/x86_64-linux-gnu/7/../../../x86_64-linux-gnu/libdl.so: error adding symbols: DSO missing from command line\r\ncollect2: error: ld returned 1 exit status\r\n```\r\nso it seems the order of libraries is wrong here (`-lhdf5` should come before `-ldl` on the command line), but I'm not sure how to go about fixing it, since everything is generated by the build system I'm not too familiar with.\r\n\r\nMy current workaround is to link against `hdf5` installed in the system instead (requires some manual work to set paths correctly; in particular, on Ubuntu headers go in `/usr/include/hdf5/openmpi' and libs in '/usr/lib/x86_64-linux-gnu/hdf5/openmpi'; so there is no single `HDF5_DIR` to point to).\r\n\r\nSince this doesn't happen often, this is low priority. Just wondering if anyone else is running into similar issues. My system setup is as standard as it gets and is a popular distro, so maybe worth fixing at some point."}}
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