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odelaneau / shapeit4

Segmented HAPlotype Estimation and Imputation Tool
MIT License
89 stars 17 forks source link

Fixed, -lcurl -lssl -lcrypto missing while make. and generalize PATH for EasyBuild #8

Open sinonkt opened 4 years ago

sinonkt commented 4 years ago

Hi, Here are some fixes that let me be able to build shapeit4 as easybuild config without errors. As I've try to build shapeit4 on my organization HPC and also willing to encode build process as easybuild-config one, so that I can contribute back something to EB community. I started with load modules dependencies needed.

 ml load foss/2018b 
 ml load HTSlib/1.9-foss-2018b 
 ml load Boost/1.67.0-foss-2018b

Then, I've modified your makefile to look something like this.

#HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
HTSLIB_INC=$(EBROOTHTSLIB)/include/htslib
HTSLIB_LIB=$(EBROOTHTSLIB)/lib/libhts.a

#BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
BOOST_INC=$(EBROOTBOOST)/include/boost
BOOST_LIB_IO=$(EBROOTBOOST)/lib/libboost_iostreams.a
BOOST_LIB_PO=$(EBROOTBOOST)/lib/libboost_program_options.a

which will be compatible with easybuild & modules on any HPC environment and the compilation went well except when they try to load dynamic libs, I encounter this error.

(base) [kphornsi@tara-frontend-1 shapeit4]$ make
g++ -std=c++11 -O3 obj/main.o obj/haplotype_segment.o obj/compute_job.o obj/variant.o obj/hmm_parameters.o obj/genotype_mask.o obj/genotype_sweep.o obj/genotype_prune.o obj/genotype_managment.o obj/genotype_build.o obj/genotype_reader1.o obj/gmap_reader.o obj/genotype_reader2.o obj/haplotype_writer.o obj/variant_map.o obj/genotype_set.o obj/haplotype_set.o obj/pbwt_solver.o obj/builder.o obj/phaser_initialise.o obj/phaser_finalise.o obj/phaser_management.o obj/phaser_parameters.o obj/phaser_algorithm.o /tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a /tarafs/biobank/data/modules/.local/easybuild/software/Boost/1.67.0-foss-2018b/lib/libboost_iostreams.a /tarafs/biobank/data/modules/.local/easybuild/software/Boost/1.67.0-foss-2018b/lib/libboost_program_options.a -o bin/shapeit4 -lz -lbz2 -lm -lpthread -llzma
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function easy_errno: error: undefined reference to 'curl_easy_getinfo'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function easy_errno: error: undefined reference to 'curl_easy_getinfo'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function wait_perform: error: undefined reference to 'curl_multi_fdset'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function wait_perform: error: undefined reference to 'curl_multi_perform'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function wait_perform: error: undefined reference to 'curl_multi_info_read'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function wait_perform: error: undefined reference to 'curl_multi_timeout'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_close: error: undefined reference to 'curl_easy_pause'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_close: error: undefined reference to 'curl_multi_remove_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_close: error: undefined reference to 'curl_easy_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_close: error: undefined reference to 'curl_multi_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_close: error: undefined reference to 'curl_multi_remove_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_write: error: undefined reference to 'curl_easy_pause'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_exit: error: undefined reference to 'curl_share_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_multi_init'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_init'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_multi_add_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_multi_remove_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_multi_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_open: error: undefined reference to 'curl_easy_getinfo'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_duphandle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_pause'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_multi_remove_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_reset'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_multi_add_handle'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_reset'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function restart_from_position: error: undefined reference to 'curl_easy_reset'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_read: error: undefined reference to 'curl_easy_pause'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_global_init'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_init'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_setopt'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_version_info'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_global_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_share_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function hfile_plugin_init_libcurl: error: undefined reference to 'curl_global_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_libcurl.o):hfile_libcurl.c:function libcurl_exit: error: undefined reference to 'curl_global_cleanup'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_s3.o):hfile_s3.c:function auth_header_callback: error: undefined reference to 'EVP_sha1'
/tarafs/biobank/data/modules/.local/easybuild/software/HTSlib/1.9-foss-2018b/lib/libhts.a(hfile_s3.o):hfile_s3.c:function auth_header_callback: error: undefined reference to 'HMAC'
collect2: error: ld returned 1 exit status
make: *** [bin/shapeit4] Error 1

It can be solved by adding a missing libs -lcurl -lssl -lcrypto like these

#DYNAMIC LIBRARIES
DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto

So now build process was successful and compatible with this following easyconfig for furthur pull request over easybuild community together. sinonkt/easybuild-easyconfigs#shapeit4 I'm really new when comes to contribute to open source. please advices me if there is anything i can improve. Thank you in advance. Hope this help! :))

Deleetdk commented 3 years ago 
#DYNAMIC LIBRARIES
DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto

Fixed the issue for me as well (Mint 20.04).

verdurin commented 3 years ago

I've submitted an updated easyconfig including a patch to remove the hard-coded build settings.

It's at:

https://github.com/easybuilders/easybuild-easyconfigs/pull/12187