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cooperative-computing-lab / cctools

The Cooperative Computing Tools (cctools) enable large scale distributed computations to harness hundreds to thousands of machines from clusters, clouds, and grids.
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cctools compile error in OSX 10.10 #691

Closed ajmazurie closed 9 years ago

ajmazurie commented 9 years ago

Hi, I'm trying to compile cctools 4.3.2 on my OSX 10.10.2 box, and get the following error message:

> make install
COMPILE auth.o
COMPILE auth_address.o
COMPILE auth_all.o
...
COMPILE get_line.o
COMPILE getopt.o
COMPILE getopt_aux.o
In file included from getopt_aux.c:13:
In file included from /Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt_aux.h:9:
/Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt.h:10:10: fatal error: 
      '/usr/include/getopt.h' file not found
#include </usr/include/getopt.h>
         ^
1 error generated.
make[2]: *** [getopt_aux.o] Error 1
make[1]: *** [src] Error 2
make: *** [dttools] Error 2

I could of course edit getopt_aux.h, but I'd want to be sure this is the right way to fix this problem.

Best, Aurelien

haiyanmeng commented 9 years ago

Hi Aurelien, Thanks for your report. We will give it a look.

Best, Haiyan

On Tue, Mar 24, 2015 at 11:56 AM, Aurélien Mazurie, Ph.D. < notifications@github.com> wrote:

Hi, I'm trying to compile cctools 4.3.2 on my OSX 10.10.2 box, and get the following error message:

make install COMPILE auth.o COMPILE auth_address.o COMPILE auth_all.o ... COMPILE get_line.o COMPILE getopt.o COMPILE getopt_aux.o In file included from getopt_aux.c:13: In file included from /Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt_aux.h:9: /Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt.h:10:10: fatal error: '/usr/include/getopt.h' file not found#include </usr/include/getopt.h> ^ 1 error generated. make[2]: * [getopt_aux.o] Error 1 make[1]: * [src] Error 2 make: *\ [dttools] Error 2

I could of course edit getopt_aux.h, but I'd want to be sure this is the right way to fix this problem.

Best, Aurelien

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691.

pivie commented 9 years ago

Haiyan, Aurelien,

Since I have a mac, why don't I see if I can reproduce it.

On Tue, Mar 24, 2015 at 12:19 PM, hmeng-19 notifications@github.com wrote:

Hi Aurelien, Thanks for your report. We will give it a look.

Best, Haiyan

On Tue, Mar 24, 2015 at 11:56 AM, Aurélien Mazurie, Ph.D. < notifications@github.com> wrote:

Hi, I'm trying to compile cctools 4.3.2 on my OSX 10.10.2 box, and get the following error message:

make install COMPILE auth.o COMPILE auth_address.o COMPILE auth_all.o ... COMPILE get_line.o COMPILE getopt.o COMPILE getopt_aux.o In file included from getopt_aux.c:13: In file included from /Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt_aux.h:9:

/Users/ajmazurie/Downloads/cctools-4.3.2-source/dttools/src/getopt.h:10:10: fatal error: '/usr/include/getopt.h' file not found#include </usr/include/getopt.h> ^ 1 error generated. make[2]: * [getopt_aux.o] Error 1 make[1]: * [src] Error 2 make: *\ [dttools] Error 2

I could of course edit getopt_aux.h, but I'd want to be sure this is the right way to fix this problem.

Best, Aurelien

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-85587304 .

dthain commented 9 years ago

@pivie thanks for the offer, please look at this one while @hmeng-19 works on the makeflow segfault.

pivie commented 9 years ago

I ran the following commands: wget http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz tar xvf cctools-4.3.2-source.tar.gz ./configure make make install

But I didn't get an error. I included the full console log below in case it will help. It is possible I installed some package on my machine in the past that made things work. I will try to find a clean OSX install to try it on.

Console log: goliath:Downloads pivie$ wget http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz --2015-03-25 09:10:42-- http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz Resolving ccl.cse.nd.edu... 129.74.152.167 Connecting to ccl.cse.nd.edu|129.74.152.167|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3499927 (3.3M) [application/x-gzip] Saving to: 'cctools-4.3.2-source.tar.gz'

100%[========================================================================================================================================>] 3,499,927 14.1MB/s in 0.2s

2015-03-25 09:10:42 (14.1 MB/s) - 'cctools-4.3.2-source.tar.gz' saved [3499927/3499927]

goliath:Downloads pivie$ tar xvf cctools-4.3.2-source.tar.gz x cctools-4.3.2-source/ x cctools-4.3.2-source/.gitignore x cctools-4.3.2-source/.module.mk x cctools-4.3.2-source/COPYING x cctools-4.3.2-source/CREDITS x cctools-4.3.2-source/Makefile x cctools-4.3.2-source/README x cctools-4.3.2-source/README.debian x cctools-4.3.2-source/allpairs/ x cctools-4.3.2-source/allpairs/Makefile x cctools-4.3.2-source/allpairs/src.tpds/ x cctools-4.3.2-source/allpairs/src.tpds/.gitignore x cctools-4.3.2-source/allpairs/src.tpds/Makefile x cctools-4.3.2-source/allpairs/src.tpds/allpairs.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_cleanup.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_status.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_wait.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_wrapper.sh x cctools-4.3.2-source/allpairs/src.tpds/ragged_array.c x cctools-4.3.2-source/allpairs/src.tpds/ragged_array.h x cctools-4.3.2-source/allpairs/src/ x cctools-4.3.2-source/allpairs/src/.gitignore x cctools-4.3.2-source/allpairs/src/Makefile x cctools-4.3.2-source/allpairs/src/allpairs_compare.c x cctools-4.3.2-source/allpairs/src/allpairs_compare.h x cctools-4.3.2-source/allpairs/src/allpairs_master.c x cctools-4.3.2-source/allpairs/src/allpairs_multicore.c x cctools-4.3.2-source/allpairs/test/ x cctools-4.3.2-source/allpairs/test/README x cctools-4.3.2-source/allpairs/test/TR_allpairs_bitwise.sh x cctools-4.3.2-source/allpairs/test/TR_allpairs_composite.sh x cctools-4.3.2-source/allpairs/test/composites.txt x cctools-4.3.2-source/allpairs/test/divisible.sh x cctools-4.3.2-source/allpairs/test/gen_ints.sh x cctools-4.3.2-source/allpairs/test/lc_compare.sh x cctools-4.3.2-source/allpairs/test/set.list x cctools-4.3.2-source/apps/ x cctools-4.3.2-source/apps/Makefile x cctools-4.3.2-source/apps/README x cctools-4.3.2-source/apps/makeflow_blast/ x cctools-4.3.2-source/apps/makeflow_blast/README x cctools-4.3.2-source/apps/makeflow_blast/makeflow_blast x cctools-4.3.2-source/apps/makeflow_bwa/ x cctools-4.3.2-source/apps/makeflow_bwa/README x cctools-4.3.2-source/apps/makeflow_bwa/makeflow_bwa x cctools-4.3.2-source/apps/parrot_atlas/ x cctools-4.3.2-source/apps/parrot_atlas/PhysicsAnalysis.tar.gz x cctools-4.3.2-source/apps/parrot_atlas/README x cctools-4.3.2-source/apps/parrot_atlas/atlas.sh x cctools-4.3.2-source/apps/parrot_atlas/parrot.atlas.sh x cctools-4.3.2-source/apps/parrot_cms/ x cctools-4.3.2-source/apps/parrot_cms/README x cctools-4.3.2-source/apps/parrot_cms/SITECONF/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/site-local-config.xml x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/site-local-config.xml.orig x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/PhEDEx/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/PhEDEx/storage.xml x cctools-4.3.2-source/apps/parrot_cms/cmsjob.sh x cctools-4.3.2-source/apps/parrot_cms/parrot.cmsjob.sh x cctools-4.3.2-source/apps/wq_maker/ x cctools-4.3.2-source/apps/wq_maker/README x cctools-4.3.2-source/apps/wq_maker/wq_maker x cctools-4.3.2-source/apps/wq_replica_exchange/ x cctools-4.3.2-source/apps/wq_replica_exchange/Makefile x cctools-4.3.2-source/apps/wq_replica_exchange/README x cctools-4.3.2-source/apps/wq_replica_exchange/par_all27_prot_lipid.inp x cctools-4.3.2-source/apps/wq_replica_exchange/protomol_functions.py x cctools-4.3.2-source/apps/wq_replica_exchange/wq_replica_exchange x cctools-4.3.2-source/apps/wq_replica_exchange/ww_exteq_nowater1.pdb x cctools-4.3.2-source/apps/wq_replica_exchange/ww_exteq_nowater1.psf x cctools-4.3.2-source/apps/wq_sort/ x cctools-4.3.2-source/apps/wq_sort/Makefile x cctools-4.3.2-source/apps/wq_sort/README x cctools-4.3.2-source/apps/wq_sort/sample.txt x cctools-4.3.2-source/apps/wq_sort/wq_sort.c x cctools-4.3.2-source/cctools.indent x cctools-4.3.2-source/chirp/ x cctools-4.3.2-source/chirp/Makefile x cctools-4.3.2-source/chirp/src/ x cctools-4.3.2-source/chirp/src/.gitignore x cctools-4.3.2-source/chirp/src/Makefile x cctools-4.3.2-source/chirp/src/chirp_acl.c x cctools-4.3.2-source/chirp/src/chirp_acl.h x cctools-4.3.2-source/chirp/src/chirp_alloc.c x cctools-4.3.2-source/chirp/src/chirp_alloc.h x cctools-4.3.2-source/chirp/src/chirp_audit.c x cctools-4.3.2-source/chirp/src/chirp_audit.h x cctools-4.3.2-source/chirp/src/chirp_audit_cluster x cctools-4.3.2-source/chirp/src/chirp_benchmark.c x cctools-4.3.2-source/chirp/src/chirp_client.c x cctools-4.3.2-source/chirp/src/chirp_client.h x cctools-4.3.2-source/chirp/src/chirp_distribute.c x cctools-4.3.2-source/chirp/src/chirp_filesystem.c x cctools-4.3.2-source/chirp/src/chirp_filesystem.h x cctools-4.3.2-source/chirp/src/chirp_fs_chirp.c x cctools-4.3.2-source/chirp/src/chirp_fs_chirp.h x cctools-4.3.2-source/chirp/src/chirp_fs_hdfs.c x cctools-4.3.2-source/chirp/src/chirp_fs_hdfs.h x cctools-4.3.2-source/chirp/src/chirp_fs_local.c x cctools-4.3.2-source/chirp/src/chirp_fs_local.h x cctools-4.3.2-source/chirp/src/chirp_fs_local_scheduler.c x cctools-4.3.2-source/chirp/src/chirp_fs_local_scheduler.h x cctools-4.3.2-source/chirp/src/chirp_fuse.c x cctools-4.3.2-source/chirp/src/chirp_get.c x cctools-4.3.2-source/chirp/src/chirp_global.c x cctools-4.3.2-source/chirp/src/chirp_global.h x cctools-4.3.2-source/chirp/src/chirp_group.c x cctools-4.3.2-source/chirp/src/chirp_group.h x cctools-4.3.2-source/chirp/src/chirp_job.c x cctools-4.3.2-source/chirp/src/chirp_job.h x cctools-4.3.2-source/chirp/src/chirp_matrix.c x cctools-4.3.2-source/chirp/src/chirp_matrix.h x cctools-4.3.2-source/chirp/src/chirp_matrix_benchmark.c x cctools-4.3.2-source/chirp/src/chirp_matrix_roc.c x cctools-4.3.2-source/chirp/src/chirp_multi.c x cctools-4.3.2-source/chirp/src/chirp_matrix_verify.c x cctools-4.3.2-source/chirp/src/chirp_multi.h x cctools-4.3.2-source/chirp/src/chirp_protocol.h x cctools-4.3.2-source/chirp/src/chirp_put.c x cctools-4.3.2-source/chirp/src/chirp_recursive.c x cctools-4.3.2-source/chirp/src/chirp_recursive.h x cctools-4.3.2-source/chirp/src/chirp_reli.c x cctools-4.3.2-source/chirp/src/chirp_reli.h x cctools-4.3.2-source/chirp/src/chirp_server.c x cctools-4.3.2-source/chirp/src/chirp_server_hdfs x cctools-4.3.2-source/chirp/src/chirp_sqlite.h x cctools-4.3.2-source/chirp/src/chirp_stats.c x cctools-4.3.2-source/chirp/src/chirp_stats.h x cctools-4.3.2-source/chirp/src/chirp_status.c x cctools-4.3.2-source/chirp/src/chirp_stream.c x cctools-4.3.2-source/chirp/src/chirp_stream.h x cctools-4.3.2-source/chirp/src/chirp_stream_files.c x cctools-4.3.2-source/chirp/src/chirp_thirdput.c x cctools-4.3.2-source/chirp/src/chirp_thirdput.h x cctools-4.3.2-source/chirp/src/chirp_ticket.c x cctools-4.3.2-source/chirp/src/chirp_ticket.h x cctools-4.3.2-source/chirp/src/chirp_tool.c x cctools-4.3.2-source/chirp/src/chirp_types.h x cctools-4.3.2-source/chirp/src/sqlite3.c x cctools-4.3.2-source/chirp/src/sqlite3.h x cctools-4.3.2-source/chirp/test/ x cctools-4.3.2-source/chirp/test/TR_chirp_acl.sh x cctools-4.3.2-source/chirp/test/TR_chirp_alloc.sh x cctools-4.3.2-source/chirp/test/TR_chirp_benchmark.sh x cctools-4.3.2-source/chirp/test/TR_chirp_hdfs.sh x cctools-4.3.2-source/chirp/test/TR_chirp_job.sh x cctools-4.3.2-source/chirp/test/TR_chirp_multi.sh x cctools-4.3.2-source/chirp/test/TR_chirp_ops.sh x cctools-4.3.2-source/chirp/test/TR_chirp_proxy.sh x cctools-4.3.2-source/chirp/test/TR_chirp_rmall.sh x cctools-4.3.2-source/chirp/test/TR_chirp_search.sh x cctools-4.3.2-source/chirp/test/TR_chirp_thirdput.sh x cctools-4.3.2-source/chirp/test/TR_chirp_tickets.sh x cctools-4.3.2-source/chirp/test/chirp-common.sh x cctools-4.3.2-source/configure x cctools-4.3.2-source/configure.afs x cctools-4.3.2-source/configure.tools x cctools-4.3.2-source/contrib/ x cctools-4.3.2-source/contrib/README x cctools-4.3.2-source/contrib/lpw-scripts/ x cctools-4.3.2-source/contrib/lpw-scripts/biox3/ x cctools-4.3.2-source/contrib/lpw-scripts/biox3/saturate-gpu x cctools-4.3.2-source/contrib/lpw-scripts/biox3/torque_submit_workers_gpu x cctools-4.3.2-source/contrib/lpw-scripts/biox3/torque_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/certainty/ x cctools-4.3.2-source/contrib/lpw-scripts/certainty/torque_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/proclus/ x cctools-4.3.2-source/contrib/lpw-scripts/proclus/sge_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/stampede/ x cctools-4.3.2-source/contrib/lpw-scripts/stampede/submit_workers_gpu x cctools-4.3.2-source/contrib/lpw-scripts/vsp-compute/ x cctools-4.3.2-source/contrib/lpw-scripts/vsp-compute/torque_submit_workers_lp x cctools-4.3.2-source/deltadb/ x cctools-4.3.2-source/deltadb/Makefile x cctools-4.3.2-source/deltadb/src/ x cctools-4.3.2-source/deltadb/src/Makefile x cctools-4.3.2-source/deltadb/src/README x cctools-4.3.2-source/deltadb/src/deltadb_collect.c x cctools-4.3.2-source/deltadb/src/deltadb_pivot.c x cctools-4.3.2-source/deltadb/src/deltadb_project.c x cctools-4.3.2-source/deltadb/src/deltadb_reduce_spatial.c x cctools-4.3.2-source/deltadb/src/deltadb_reduce_temporal.c x cctools-4.3.2-source/deltadb/src/deltadb_reduction.c x cctools-4.3.2-source/deltadb/src/deltadb_reduction.h x cctools-4.3.2-source/deltadb/src/deltadb_select_complete.c x cctools-4.3.2-source/deltadb/src/deltadb_select_dynamic.c x cctools-4.3.2-source/deltadb/src/deltadb_select_static.c x cctools-4.3.2-source/deltadb/src/python-old/ x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_count x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_filter x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_plot x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_read_and_print x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_select x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_stream x cctools-4.3.2-source/deltadb/test/ x cctools-4.3.2-source/deltadb/test/query1.sh x cctools-4.3.2-source/deltadb/test/query2.sh x cctools-4.3.2-source/deltadb/test/query3.sh x cctools-4.3.2-source/doc/ x cctools-4.3.2-source/doc/.gitignore x cctools-4.3.2-source/doc/Makefile x cctools-4.3.2-source/doc/allpairs.html x cctools-4.3.2-source/doc/awe.html x cctools-4.3.2-source/doc/awe/ x cctools-4.3.2-source/doc/awe/ala-rama-awe.png x cctools-4.3.2-source/doc/awe/ala-rama-msm.png x cctools-4.3.2-source/doc/awe/flowchart.png x cctools-4.3.2-source/doc/awe/walkers.png x cctools-4.3.2-source/doc/awe/workflow.png x cctools-4.3.2-source/doc/cctools.doxygen x cctools-4.3.2-source/doc/cctools.doxygen.config x cctools-4.3.2-source/doc/chirp.html x 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cctools-4.3.2-source/resource_monitor/src/cluster.c x cctools-4.3.2-source/resource_monitor/src/histograms.c x cctools-4.3.2-source/resource_monitor/src/piggybacker.c x cctools-4.3.2-source/resource_monitor/src/resource_monitor.c x cctools-4.3.2-source/resource_monitor/src/resource_monitor_cluster.c x cctools-4.3.2-source/resource_monitor/src/resource_monitor_histograms.c x cctools-4.3.2-source/resource_monitor/src/rmon_tools.c x cctools-4.3.2-source/resource_monitor/src/rmon_tools.h x cctools-4.3.2-source/resource_monitor/src/rmonitor_helper.c x cctools-4.3.2-source/resource_monitor/src/rmonitor_helper_comm.c x cctools-4.3.2-source/resource_monitor/src/rmonitor_helper_comm.h x cctools-4.3.2-source/resource_monitor/src/rmonitor_poll.c x cctools-4.3.2-source/resource_monitor/src/rmonitor_poll.h x cctools-4.3.2-source/resource_monitor/src/rmonitor_types.h x cctools-4.3.2-source/resource_monitor/test/ x cctools-4.3.2-source/resource_monitor/test/hogmem.c x cctools-4.3.2-source/resource_monitor/test/msqrt.c x cctools-4.3.2-source/resource_monitor_visualizer/ x cctools-4.3.2-source/resource_monitor_visualizer/Makefile x cctools-4.3.2-source/resource_monitor_visualizer/src/ x cctools-4.3.2-source/resource_monitor_visualizer/src/Makefile x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer.py x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/ x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/css/ x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/css/style.css x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/img/ x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/img/arrow-next.png x cctools-4.3.2-source/resource_monitor_visualizer/src/resource_monitor_visualizer_static/img/arrow-prev.png x 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cctools-4.3.2-source/s3tools/src/s3c_file.c x cctools-4.3.2-source/s3tools/src/s3c_file.h x cctools-4.3.2-source/s3tools/src/s3c_util.c x cctools-4.3.2-source/s3tools/src/s3c_util.h x cctools-4.3.2-source/s3tools/src/s3client.h x cctools-4.3.2-source/s3tools/src/s3common.c x cctools-4.3.2-source/s3tools/src/s3common.h x cctools-4.3.2-source/s3tools/src/s3get.c x cctools-4.3.2-source/s3tools/src/s3getacl.c x cctools-4.3.2-source/s3tools/src/s3ls.c x cctools-4.3.2-source/s3tools/src/s3mkdir.c x cctools-4.3.2-source/s3tools/src/s3put.c x cctools-4.3.2-source/s3tools/src/s3rm.c x cctools-4.3.2-source/s3tools/src/s3rmdir.c x cctools-4.3.2-source/s3tools/src/s3setacl.c x cctools-4.3.2-source/s3tools/src/s3stat.c x cctools-4.3.2-source/sand/ x cctools-4.3.2-source/sand/.gitignore x cctools-4.3.2-source/sand/Makefile x cctools-4.3.2-source/sand/src/ x cctools-4.3.2-source/sand/src/.gitignore x cctools-4.3.2-source/sand/src/Makefile x cctools-4.3.2-source/sand/src/align.c x cctools-4.3.2-source/sand/src/align.h x cctools-4.3.2-source/sand/src/compressed_sequence.c x cctools-4.3.2-source/sand/src/compressed_sequence.h x cctools-4.3.2-source/sand/src/matrix.c x cctools-4.3.2-source/sand/src/matrix.h x cctools-4.3.2-source/sand/src/overlap.c x cctools-4.3.2-source/sand/src/overlap.h x cctools-4.3.2-source/sand/src/sand_align_kernel.c x cctools-4.3.2-source/sand/src/sand_align_master.c x cctools-4.3.2-source/sand/src/sand_compress_reads.c x cctools-4.3.2-source/sand/src/sand_filter_kernel.c x cctools-4.3.2-source/sand/src/sand_filter_master.c x cctools-4.3.2-source/sand/src/sand_runCA_5.4 x cctools-4.3.2-source/sand/src/sand_runCA_6.1 x cctools-4.3.2-source/sand/src/sand_runCA_7.0 x cctools-4.3.2-source/sand/src/sand_uncompress_reads.c x cctools-4.3.2-source/sand/src/sequence.c x cctools-4.3.2-source/sand/src/sequence.h x cctools-4.3.2-source/sand/src/sequence_filter.c x cctools-4.3.2-source/sand/src/sequence_filter.h x cctools-4.3.2-source/sand/test/ x cctools-4.3.2-source/sand/test/README x cctools-4.3.2-source/sand/test/TR_filter_verification.sh x cctools-4.3.2-source/sand/test/TR_sanity.sh x cctools-4.3.2-source/sand/test/filter_verification/ x cctools-4.3.2-source/sand/test/filter_verification/gen_random_reads.pl x cctools-4.3.2-source/sand/test/filter_verification/gen_random_sequence.pl x cctools-4.3.2-source/sand/test/filter_verification/verify_candidates.pl x cctools-4.3.2-source/sand/test/sand_sanity/ x cctools-4.3.2-source/sand/test/sand_sanity/test.banded.right x cctools-4.3.2-source/sand/test/sand_sanity/test.cand.right x cctools-4.3.2-source/sand/test/sand_sanity/test.fa x cctools-4.3.2-source/sand/test/sand_sanity/test.sw.right x cctools-4.3.2-source/wavefront/ x cctools-4.3.2-source/wavefront/Makefile x cctools-4.3.2-source/wavefront/example/ x cctools-4.3.2-source/wavefront/example/README x cctools-4.3.2-source/wavefront/example/example.func.c x cctools-4.3.2-source/wavefront/example/example.input.data x 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x cctools-4.3.2-source/weaver/examples/bxgrid.py x cctools-4.3.2-source/weaver/examples/collect.py x cctools-4.3.2-source/weaver/examples/functions.py x cctools-4.3.2-source/weaver/examples/group.py x cctools-4.3.2-source/weaver/examples/iterate.py x cctools-4.3.2-source/weaver/examples/iteration.py x cctools-4.3.2-source/weaver/examples/map.py x cctools-4.3.2-source/weaver/examples/mapreduce.py x cctools-4.3.2-source/weaver/examples/merge.py x cctools-4.3.2-source/weaver/examples/nests.py x cctools-4.3.2-source/weaver/examples/options.py x cctools-4.3.2-source/weaver/examples/query.py x cctools-4.3.2-source/weaver/examples/scripts.py x cctools-4.3.2-source/weaver/examples/stash.py x cctools-4.3.2-source/weaver/examples/subnests.py x cctools-4.3.2-source/weaver/examples/workbench.py x cctools-4.3.2-source/weaver/setup.py x cctools-4.3.2-source/weaver/tests.py x cctools-4.3.2-source/weaver/weaver.py x cctools-4.3.2-source/weaver/weaver/ x cctools-4.3.2-source/weaver/weaver/__init.py x 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cctools-4.3.2-source/work_queue/src/Makefile x cctools-4.3.2-source/work_queue/src/batch_job.c x cctools-4.3.2-source/work_queue/src/batch_job.h x cctools-4.3.2-source/work_queue/src/batch_job_chirp.c x cctools-4.3.2-source/work_queue/src/batch_job_cluster.c x cctools-4.3.2-source/work_queue/src/batch_job_condor.c x cctools-4.3.2-source/work_queue/src/batch_job_hadoop.c x cctools-4.3.2-source/work_queue/src/batch_job_internal.h x cctools-4.3.2-source/work_queue/src/batch_job_local.c x cctools-4.3.2-source/work_queue/src/batch_job_work_queue.c x cctools-4.3.2-source/work_queue/src/condor_submit_workers x cctools-4.3.2-source/work_queue/src/ec2_remove_workers x cctools-4.3.2-source/work_queue/src/ec2_submit_workers x cctools-4.3.2-source/work_queue/src/mpi_queue_worker.c x cctools-4.3.2-source/work_queue/src/pbs_submit_workers x cctools-4.3.2-source/work_queue/src/perl/ x cctools-4.3.2-source/work_queue/src/perl/.gitignore x cctools-4.3.2-source/work_queue/src/perl/Makefile x 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cctools-4.3.2-source/work_queue/src/python/work_queue_example.py x cctools-4.3.2-source/work_queue/src/python3/ x cctools-4.3.2-source/work_queue/src/python3/.gitignore x cctools-4.3.2-source/work_queue/src/python3/Makefile x cctools-4.3.2-source/work_queue/src/python3/work_queue.binding.py x cctools-4.3.2-source/work_queue/src/python3/work_queue.i x cctools-4.3.2-source/work_queue/src/python3/work_queue_example.py x cctools-4.3.2-source/work_queue/src/sge_submit_workers x cctools-4.3.2-source/work_queue/src/slurm_submit_workers x cctools-4.3.2-source/work_queue/src/torque_submit_workers x cctools-4.3.2-source/work_queue/src/trickle.sh x cctools-4.3.2-source/work_queue/src/work_queue.c x cctools-4.3.2-source/work_queue/src/work_queue.h x cctools-4.3.2-source/work_queue/src/work_queue.i x cctools-4.3.2-source/work_queue/src/work_queue_benchmark.sh x cctools-4.3.2-source/work_queue/src/work_queue_catalog.c x cctools-4.3.2-source/work_queue/src/work_queue_catalog.h x cctools-4.3.2-source/work_queue/src/work_queue_example.c x cctools-4.3.2-source/work_queue/src/work_queue_graph_log x cctools-4.3.2-source/work_queue/src/work_queue_internal.h x cctools-4.3.2-source/work_queue/src/work_queue_pool.c x cctools-4.3.2-source/work_queue/src/work_queue_pool.conf.example x cctools-4.3.2-source/work_queue/src/work_queue_priority_test.c x cctools-4.3.2-source/work_queue/src/work_queue_process.c x cctools-4.3.2-source/work_queue/src/work_queue_process.h x cctools-4.3.2-source/work_queue/src/work_queue_protocol.h x cctools-4.3.2-source/work_queue/src/work_queue_resources.c x cctools-4.3.2-source/work_queue/src/work_queue_resources.h x cctools-4.3.2-source/work_queue/src/work_queue_status.c x cctools-4.3.2-source/work_queue/src/work_queue_test.c x cctools-4.3.2-source/work_queue/src/work_queue_test_main.c x cctools-4.3.2-source/work_queue/src/work_queue_test_watch.c x cctools-4.3.2-source/work_queue/src/work_queue_watcher.c x cctools-4.3.2-source/work_queue/src/work_queue_watcher.h x cctools-4.3.2-source/work_queue/src/work_queue_worker.c x cctools-4.3.2-source/work_queue/src/wq_submit_workers.common x cctools-4.3.2-source/work_queue/test/ x cctools-4.3.2-source/work_queue/test/TR_work_queue_foreman.sh x cctools-4.3.2-source/work_queue/test/TR_work_queue_multicore.sh x cctools-4.3.2-source/work_queue/test/TR_work_queue_single.sh x cctools-4.3.2-source/work_queue/test/work_queue_common.sh tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/b/c/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/b/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/_acl) failed: No such file or directory goliath:Downloads pivie$ ./configure Darwin Goliath.local 14.1.0 Darwin Kernel Version 14.1.0: Thu Feb 26 19:26:47 PST 2015; root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64 checking for package compatibility... parrot is NOT supported on DARWIN for any cpu type resource_monitor IS supported on DARWIN checking for multiarch environment...no checking for all the things I know how to build... package dttools found package makeflow found package work_queue found package sand found package allpairs found package wavefront found package ftp_lite found package resource_monitor found package resource_monitor_visualizer found package makeflow_linker found package chirp found package weaver found package doc found checking for gcc.../usr/bin/gcc checking for g++.../usr/bin/g++ checking for GNU make in several places... checking for make.../usr/bin/make checking if make is GNU make...yes checking if gcc supports -Wno-unused-parameter...yes checking if gcc supports -Wno-unknown-pragmas...yes checking if gcc supports -Wno-deprecated-declarations...yes checking if gcc supports -Wno-unused-const-variable...yes checking if ld supports the --as-needed flag...no using a globus flavor of 'gcc64' (if this is wrong, use the --globus-flavor argument) checking for /usr/include/gcc64/globus_common.h...no checking for /usr/include/globus/globus_common.h...no * skipping globus support * skipping irods support checking for /usr/lib/libmysqlclient.a...no checking for /usr/lib/libmysqlclient.dylib...no * skipping mysql support * skipping xrootd support * skipping cvmfs support checking for /usr/include/fuse.h...no * skipping fuse support checking for /usr/lib/libreadline.dylib...yes checking for /usr/lib/libncurses.dylib...yes checking for /usr/lib/libtermcap.dylib...yes checking for /usr/lib/libhistory.dylib...no checking for /usr/lib/libhistory.a...no checking for /usr/bin/perl...yes perl version is 5.18.2 checking for /usr/bin/python2...no checking for /usr/bin/python...yes python version is 2.7.6 checking for /usr/include/python2.7/Python.h...yes found python development libraries python version is suitable for weaver checking for /usr/bin/python3...no checking for /usr/bin/python...yes checking for /usr/bin/2to3...yes python3 version is 2.7.6 * Sorry, we require Python3 >= 3.0 * skipping python3 support checking for /usr/bin/swig...no checking for swig...not found * skipping swig bindings for work queue checking for /usr/lib/libssl.dylib...yes checking for /usr/lib/libcrypto.dylib...yes checking for /usr/lib/libresolv.dylib...yes checking for /usr/lib/libsocket.dylib...no checking for /usr/lib/libsocket.a...no checking for /usr/lib/libnsl.dylib...no checking for /usr/lib/libnsl.a...no checking for /usr/lib/libz.dylib...yes checking for isnan in /usr/include/math.h...yes checking for pread in /usr/include/unistd.h...yes checking for pwrite in /usr/include/unistd.h...yes checking for strsignal in /usr/include/string.h...yes checking for usleep in /usr/include/unistd.h...yes checking for utime in /usr/include/utime.h...yes checking for header attr/xattr.h...no checking for header fts.h...yes checking for header inttypes.h...yes checking for header stdint.h...yes checking for header sys/statfs.h...no checking for header sys/statvfs.h...yes checking for header sys/xattr.h...yes checking for header syslog.h...yes checking for doxygen...not found *\ not building API documentation checking for m4.../usr/bin/m4 checking for nroff.../usr/bin/nroff Creating config.mk...

To re-configure, type './configure.rerun' To build, type 'make' To build and install, type 'make install'

goliath:cctools-4.3.2-source pivie$ make COMPILE auth.o COMPILE auth_address.o COMPILE auth_all.o COMPILE auth_globus.o COMPILE auth_hostname.o COMPILE auth_kerberos.o COMPILE auth_ticket.o COMPILE auth_unix.o COMPILE b64_encode.o COMPILE bitmap.o COMPILE buffer.o COMPILE catalog_query.o COMPILE cctools.o COMPILE change_process_title.o COMPILE chunk.o COMPILE clean_dir.o COMPILE console_login.o COMPILE copy_stream.o COMPILE create_dir.o COMPILE daemon.o COMPILE datagram.o COMPILE debug.o COMPILE debug_file.o COMPILE debug_journal.o COMPILE debug_stream.o COMPILE debug_syslog.o COMPILE disk_info.o COMPILE domain_name.o COMPILE domain_name_cache.o COMPILE dpopen.o COMPILE envtools.o COMPILE fast_popen.o COMPILE fd.o COMPILE file_cache.o COMPILE full_io.o COMPILE get_canonical_path.o COMPILE get_line.o COMPILE getopt.o COMPILE getopt_aux.o COMPILE gpu_info.o COMPILE hash_cache.o COMPILE hash_table.o COMPILE hdfs_library.o COMPILE hmac.o COMPILE http_query.o COMPILE itable.o COMPILE json.o COMPILE json_aux.o COMPILE link.o COMPILE link_auth.o COMPILE link_nvpair.o COMPILE list.o COMPILE load_average.o COMPILE md5.o COMPILE memory_info.o COMPILE mergesort.o COMPILE nvpair.o COMPILE nvpair_database.o COMPILE password_cache.o COMPILE path.o COMPILE pattern.o COMPILE preadwrite.o COMPILE process.o COMPILE random_init.o COMPILE rmonitor.o COMPILE rmsummary.o COMPILE set.o COMPILE sha1.o COMPILE sleeptools.o COMPILE sort_dir.o COMPILE string_array.o COMPILE stringtools.o COMPILE text_array.o COMPILE text_list.o COMPILE timer.o COMPILE timestamp.o COMPILE unlink_recursive.o COMPILE uptime.o COMPILE url_encode.o COMPILE username.o COMPILE xxmalloc.o ar rv libdttools.a auth.o auth_address.o auth_all.o auth_globus.o auth_hostname.o auth_kerberos.o auth_ticket.o auth_unix.o b64_encode.o bitmap.o buffer.o catalog_query.o cctools.o change_process_title.o chunk.o clean_dir.o console_login.o copy_stream.o create_dir.o daemon.o datagram.o debug.o debug_file.o debug_journal.o debug_stream.o debug_syslog.o disk_info.o domain_name.o domain_name_cache.o dpopen.o envtools.o fast_popen.o fd.o file_cache.o full_io.o get_canonical_path.o get_line.o getopt.o getopt_aux.o gpu_info.o hash_cache.o hash_table.o hdfs_library.o hmac.o http_query.o itable.o json.o json_aux.o link.o link_auth.o link_nvpair.o list.o load_average.o md5.o memory_info.o mergesort.o nvpair.o nvpair_database.o password_cache.o path.o pattern.o preadwrite.o process.o random_init.o rmonitor.o rmsummary.o set.o sha1.o sleeptools.o sort_dir.o string_array.o stringtools.o text_array.o text_list.o timer.o timestamp.o unlink_recursive.o uptime.o url_encode.o username.o xxmalloc.o ar: creating archive libdttools.a a - auth.o a - auth_address.o a - auth_all.o a - auth_globus.o a - auth_hostname.o a - auth_kerberos.o a - auth_ticket.o a - auth_unix.o a - b64_encode.o a - bitmap.o a - buffer.o a - catalog_query.o a - cctools.o a - change_process_title.o a - chunk.o a - clean_dir.o a - console_login.o a - copy_stream.o a - create_dir.o a - daemon.o a - datagram.o a - debug.o a - debug_file.o a - debug_journal.o a - debug_stream.o a - debug_syslog.o a - disk_info.o a - domain_name.o a - domain_name_cache.o a - dpopen.o a - envtools.o a - fast_popen.o a - fd.o a - file_cache.o a - full_io.o a - get_canonical_path.o a - get_line.o a - getopt.o a - getopt_aux.o a - gpu_info.o a - hash_cache.o a - hash_table.o a - hdfs_library.o a - hmac.o a - http_query.o a - itable.o a - json.o a - json_aux.o a - link.o a - link_auth.o a - link_nvpair.o a - list.o a - load_average.o a - md5.o a - memory_info.o a - mergesort.o a - nvpair.o a - nvpair_database.o a - password_cache.o a - path.o a - pattern.o a - preadwrite.o a - process.o a - random_init.o a - rmonitor.o a - rmsummary.o a - set.o a - sha1.o a - sleeptools.o a - sort_dir.o a - string_array.o a - stringtools.o a - text_array.o a - text_list.o a - timer.o a - timestamp.o a - unlink_recursive.o a - uptime.o a - url_encode.o a - username.o a - xxmalloc.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(debug_journal.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(getopt.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(preadwrite.o) has no symbols ranlib libdttools.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(debug_journal.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(getopt.o) has no symbols /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libdttools.a(preadwrite.o) has no symbols COMPILE catalog_update.o LINK catalog_update COMPILE catalog_server.o LINK catalog_server COMPILE watchdog.o LINK watchdog COMPILE auth_test.o LINK auth_test COMPILE microbench.o LINK microbench COMPILE multirun.o LINK multirun rm watchdog

ajmazurie commented 9 years ago

I confirm that by re-running the same commands I do get the abovementioned error on my 10.10.2 box.

haiyanmeng commented 9 years ago

Hi Aurélien, I just found a MAC machine with the version of 10.9.5. Here is the configuration of the the machine I used: _cclmac02:~ hmeng$ swvers -productVersion 10.9.5 cclmac02:~ hmeng$ uname -a _Darwin cclmac02.cse.nd.edu http://cclmac02.cse.nd.edu 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x8664

Unfortunately, I can not reproduce your problem. For now, I have two suggestions: 1) Redownload cctools-4.3.3-source.tar.gz from http://ccl.cse.nd.edu/software/downloadfiles.php , (Ben has fixed the makeflow -f problem in the new source code), and recompile it: ./configure --prefix ~/cctools make clean make install 2) Run gcc -v -E - on your machine to see the include search path. Here is the output of the command gcc -v -E -, you can run the command on you MAC to see the include search path, and to check whether there is a getopt.h file which can be found by gcc. cclmac02:cctools-4.3.3-source hmeng$ gcc -v -E - Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) _Target: x8664-apple-darwin13.4.0 Thread model: posix

Let us know if you still have problems. Sorry for the late reply.

Best, Haiyan

On Wed, Mar 25, 2015 at 12:46 PM, Aurélien Mazurie, Ph.D. < notifications@github.com> wrote:

I confirm that by re-running the same commands I do get an error on my 10.10.2 box. Aurélien

On Mar 25, 2015, at 7:38 AM, Peter Ivie notifications@github.com wrote:

I ran the following commands: wget http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz tar xvf cctools-4.3.2-source.tar.gz ./configure make make install

But I didn't get an error. I included the full console log below in case it will help. It is possible I installed some package on my machine in the past that made things work. I will try to find a clean OSX install to try it on.

Console log: goliath:Downloads pivie$ wget http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz --2015-03-25 09:10:42-- http://ccl.cse.nd.edu/software/files/cctools-4.3.2-source.tar.gz Resolving ccl.cse.nd.edu... 129.74.152.167 Connecting to ccl.cse.nd.edu|129.74.152.167|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3499927 (3.3M) [application/x-gzip] Saving to: 'cctools-4.3.2-source.tar.gz'

100%[========================================================================================================================================>] 3,499,927 14.1MB/s in 0.2s

2015-03-25 09:10:42 (14.1 MB/s) - 'cctools-4.3.2-source.tar.gz' saved [3499927/3499927]

goliath:Downloads pivie$ tar xvf cctools-4.3.2-source.tar.gz x cctools-4.3.2-source/ x cctools-4.3.2-source/.gitignore x cctools-4.3.2-source/.module.mk x cctools-4.3.2-source/COPYING x cctools-4.3.2-source/CREDITS x cctools-4.3.2-source/Makefile x cctools-4.3.2-source/README x cctools-4.3.2-source/README.debian x cctools-4.3.2-source/allpairs/ x cctools-4.3.2-source/allpairs/Makefile x cctools-4.3.2-source/allpairs/src.tpds/ x cctools-4.3.2-source/allpairs/src.tpds/.gitignore x cctools-4.3.2-source/allpairs/src.tpds/Makefile x cctools-4.3.2-source/allpairs/src.tpds/allpairs.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_cleanup.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_status.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_wait.c x cctools-4.3.2-source/allpairs/src.tpds/allpairs_wrapper.sh x cctools-4.3.2-source/allpairs/src.tpds/ragged_array.c x cctools-4.3.2-source/allpairs/src.tpds/ragged_array.h x cctools-4.3.2-source/allpairs/src/ x cctools-4.3.2-source/allpairs/src/.gitignore x cctools-4.3.2-source/allpairs/src/Makefile x cctools-4.3.2-source/allpairs/src/allpairs_compare.c x cctools-4.3.2-source/allpairs/src/allpairs_compare.h x cctools-4.3.2-source/allpairs/src/allpairs_master.c x cctools-4.3.2-source/allpairs/src/allpairs_multicore.c x cctools-4.3.2-source/allpairs/test/ x cctools-4.3.2-source/allpairs/test/README x cctools-4.3.2-source/allpairs/test/TR_allpairs_bitwise.sh x cctools-4.3.2-source/allpairs/test/TR_allpairs_composite.sh x cctools-4.3.2-source/allpairs/test/composites.txt x cctools-4.3.2-source/allpairs/test/divisible.sh x cctools-4.3.2-source/allpairs/test/gen_ints.sh x cctools-4.3.2-source/allpairs/test/lc_compare.sh x cctools-4.3.2-source/allpairs/test/set.list x cctools-4.3.2-source/apps/ x cctools-4.3.2-source/apps/Makefile x cctools-4.3.2-source/apps/README x cctools-4.3.2-source/apps/makeflow_blast/ x cctools-4.3.2-source/apps/makeflow_blast/README x cctools-4.3.2-source/apps/makeflow_blast/makeflow_blast x cctools-4.3.2-source/apps/makeflow_bwa/ x cctools-4.3.2-source/apps/makeflow_bwa/README x cctools-4.3.2-source/apps/makeflow_bwa/makeflow_bwa x cctools-4.3.2-source/apps/parrot_atlas/ x cctools-4.3.2-source/apps/parrot_atlas/PhysicsAnalysis.tar.gz x cctools-4.3.2-source/apps/parrot_atlas/README x cctools-4.3.2-source/apps/parrot_atlas/atlas.sh x cctools-4.3.2-source/apps/parrot_atlas/parrot.atlas.sh x cctools-4.3.2-source/apps/parrot_cms/ x cctools-4.3.2-source/apps/parrot_cms/README x cctools-4.3.2-source/apps/parrot_cms/SITECONF/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/ x

cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/site-local-config.xml x

cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/JobConfig/site-local-config.xml.orig x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/PhEDEx/ x cctools-4.3.2-source/apps/parrot_cms/SITECONF/local/PhEDEx/storage.xml x cctools-4.3.2-source/apps/parrot_cms/cmsjob.sh x cctools-4.3.2-source/apps/parrot_cms/parrot.cmsjob.sh x cctools-4.3.2-source/apps/wq_maker/ x cctools-4.3.2-source/apps/wq_maker/README x cctools-4.3.2-source/apps/wq_maker/wq_maker x cctools-4.3.2-source/apps/wq_replica_exchange/ x cctools-4.3.2-source/apps/wq_replica_exchange/Makefile x cctools-4.3.2-source/apps/wq_replica_exchange/README x cctools-4.3.2-source/apps/wq_replica_exchange/par_all27_prot_lipid.inp x cctools-4.3.2-source/apps/wq_replica_exchange/protomol_functions.py x cctools-4.3.2-source/apps/wq_replica_exchange/wq_replica_exchange x cctools-4.3.2-source/apps/wq_replica_exchange/ww_exteq_nowater1.pdb x cctools-4.3.2-source/apps/wq_replica_exchange/ww_exteq_nowater1.psf x cctools-4.3.2-source/apps/wq_sort/ x cctools-4.3.2-source/apps/wq_sort/Makefile x cctools-4.3.2-source/apps/wq_sort/README x cctools-4.3.2-source/apps/wq_sort/sample.txt x cctools-4.3.2-source/apps/wq_sort/wq_sort.c x cctools-4.3.2-source/cctools.indent x cctools-4.3.2-source/chirp/ x cctools-4.3.2-source/chirp/Makefile x cctools-4.3.2-source/chirp/src/ x cctools-4.3.2-source/chirp/src/.gitignore x cctools-4.3.2-source/chirp/src/Makefile x cctools-4.3.2-source/chirp/src/chirp_acl.c x cctools-4.3.2-source/chirp/src/chirp_acl.h x cctools-4.3.2-source/chirp/src/chirp_alloc.c x cctools-4.3.2-source/chirp/src/chirp_alloc.h x cctools-4.3.2-source/chirp/src/chirp_audit.c x cctools-4.3.2-source/chirp/src/chirp_audit.h x cctools-4.3.2-source/chirp/src/chirp_audit_cluster x cctools-4.3.2-source/chirp/src/chirp_benchmark.c x cctools-4.3.2-source/chirp/src/chirp_client.c x cctools-4.3.2-source/chirp/src/chirp_client.h x cctools-4.3.2-source/chirp/src/chirp_distribute.c x cctools-4.3.2-source/chirp/src/chirp_filesystem.c x cctools-4.3.2-source/chirp/src/chirp_filesystem.h x cctools-4.3.2-source/chirp/src/chirp_fs_chirp.c x cctools-4.3.2-source/chirp/src/chirp_fs_chirp.h x cctools-4.3.2-source/chirp/src/chirp_fs_hdfs.c x cctools-4.3.2-source/chirp/src/chirp_fs_hdfs.h x cctools-4.3.2-source/chirp/src/chirp_fs_local.c x cctools-4.3.2-source/chirp/src/chirp_fs_local.h x cctools-4.3.2-source/chirp/src/chirp_fs_local_scheduler.c x cctools-4.3.2-source/chirp/src/chirp_fs_local_scheduler.h x cctools-4.3.2-source/chirp/src/chirp_fuse.c x cctools-4.3.2-source/chirp/src/chirp_get.c x cctools-4.3.2-source/chirp/src/chirp_global.c x cctools-4.3.2-source/chirp/src/chirp_global.h x cctools-4.3.2-source/chirp/src/chirp_group.c x cctools-4.3.2-source/chirp/src/chirp_group.h x cctools-4.3.2-source/chirp/src/chirp_job.c x cctools-4.3.2-source/chirp/src/chirp_job.h x cctools-4.3.2-source/chirp/src/chirp_matrix.c x cctools-4.3.2-source/chirp/src/chirp_matrix.h x cctools-4.3.2-source/chirp/src/chirp_matrix_benchmark.c x cctools-4.3.2-source/chirp/src/chirp_matrix_roc.c x cctools-4.3.2-source/chirp/src/chirp_multi.c x cctools-4.3.2-source/chirp/src/chirp_matrix_verify.c x cctools-4.3.2-source/chirp/src/chirp_multi.h x cctools-4.3.2-source/chirp/src/chirp_protocol.h x cctools-4.3.2-source/chirp/src/chirp_put.c x cctools-4.3.2-source/chirp/src/chirp_recursive.c x cctools-4.3.2-source/chirp/src/chirp_recursive.h x cctools-4.3.2-source/chirp/src/chirp_reli.c x cctools-4.3.2-source/chirp/src/chirp_reli.h x cctools-4.3.2-source/chirp/src/chirp_server.c x cctools-4.3.2-source/chirp/src/chirp_server_hdfs x cctools-4.3.2-source/chirp/src/chirp_sqlite.h x cctools-4.3.2-source/chirp/src/chirp_stats.c x cctools-4.3.2-source/chirp/src/chirp_stats.h x cctools-4.3.2-source/chirp/src/chirp_status.c x cctools-4.3.2-source/chirp/src/chirp_stream.c x cctools-4.3.2-source/chirp/src/chirp_stream.h x cctools-4.3.2-source/chirp/src/chirp_stream_files.c x cctools-4.3.2-source/chirp/src/chirp_thirdput.c x cctools-4.3.2-source/chirp/src/chirp_thirdput.h x cctools-4.3.2-source/chirp/src/chirp_ticket.c x cctools-4.3.2-source/chirp/src/chirp_ticket.h x cctools-4.3.2-source/chirp/src/chirp_tool.c x cctools-4.3.2-source/chirp/src/chirp_types.h x cctools-4.3.2-source/chirp/src/sqlite3.c x cctools-4.3.2-source/chirp/src/sqlite3.h x cctools-4.3.2-source/chirp/test/ x cctools-4.3.2-source/chirp/test/TR_chirp_acl.sh x cctools-4.3.2-source/chirp/test/TR_chirp_alloc.sh x cctools-4.3.2-source/chirp/test/TR_chirp_benchmark.sh x cctools-4.3.2-source/chirp/test/TR_chirp_hdfs.sh x cctools-4.3.2-source/chirp/test/TR_chirp_job.sh x cctools-4.3.2-source/chirp/test/TR_chirp_multi.sh x cctools-4.3.2-source/chirp/test/TR_chirp_ops.sh x cctools-4.3.2-source/chirp/test/TR_chirp_proxy.sh x cctools-4.3.2-source/chirp/test/TR_chirp_rmall.sh x cctools-4.3.2-source/chirp/test/TR_chirp_search.sh x cctools-4.3.2-source/chirp/test/TR_chirp_thirdput.sh x cctools-4.3.2-source/chirp/test/TR_chirp_tickets.sh x cctools-4.3.2-source/chirp/test/chirp-common.sh x cctools-4.3.2-source/configure x cctools-4.3.2-source/configure.afs x cctools-4.3.2-source/configure.tools x cctools-4.3.2-source/contrib/ x cctools-4.3.2-source/contrib/README x cctools-4.3.2-source/contrib/lpw-scripts/ x cctools-4.3.2-source/contrib/lpw-scripts/biox3/ x cctools-4.3.2-source/contrib/lpw-scripts/biox3/saturate-gpu x cctools-4.3.2-source/contrib/lpw-scripts/biox3/torque_submit_workers_gpu x cctools-4.3.2-source/contrib/lpw-scripts/biox3/torque_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/certainty/ x

cctools-4.3.2-source/contrib/lpw-scripts/certainty/torque_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/proclus/ x cctools-4.3.2-source/contrib/lpw-scripts/proclus/sge_submit_workers_lp x cctools-4.3.2-source/contrib/lpw-scripts/stampede/ x cctools-4.3.2-source/contrib/lpw-scripts/stampede/submit_workers_gpu x cctools-4.3.2-source/contrib/lpw-scripts/vsp-compute/ x

cctools-4.3.2-source/contrib/lpw-scripts/vsp-compute/torque_submit_workers_lp x cctools-4.3.2-source/deltadb/ x cctools-4.3.2-source/deltadb/Makefile x cctools-4.3.2-source/deltadb/src/ x cctools-4.3.2-source/deltadb/src/Makefile x cctools-4.3.2-source/deltadb/src/README x cctools-4.3.2-source/deltadb/src/deltadb_collect.c x cctools-4.3.2-source/deltadb/src/deltadb_pivot.c x cctools-4.3.2-source/deltadb/src/deltadb_project.c x cctools-4.3.2-source/deltadb/src/deltadb_reduce_spatial.c x cctools-4.3.2-source/deltadb/src/deltadb_reduce_temporal.c x cctools-4.3.2-source/deltadb/src/deltadb_reduction.c x cctools-4.3.2-source/deltadb/src/deltadb_reduction.h x cctools-4.3.2-source/deltadb/src/deltadb_select_complete.c x cctools-4.3.2-source/deltadb/src/deltadb_select_dynamic.c x cctools-4.3.2-source/deltadb/src/deltadb_select_static.c x cctools-4.3.2-source/deltadb/src/python-old/ x cctools-4.3.2-source/deltadb/src/python-old/catalog_history_count x 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cctools-4.3.2-source/work_queue/src/python/TR_work_queue_python_detailed_example_2.sh x cctools-4.3.2-source/work_queue/src/python/work_queue.binding.py x cctools-4.3.2-source/work_queue/src/python/work_queue.i x

cctools-4.3.2-source/work_queue/src/python/work_queue_detailed_example_1.py x

cctools-4.3.2-source/work_queue/src/python/work_queue_detailed_example_2.py x cctools-4.3.2-source/work_queue/src/python/work_queue_example.py x cctools-4.3.2-source/work_queue/src/python3/ x cctools-4.3.2-source/work_queue/src/python3/.gitignore x cctools-4.3.2-source/work_queue/src/python3/Makefile x cctools-4.3.2-source/work_queue/src/python3/work_queue.binding.py x cctools-4.3.2-source/work_queue/src/python3/work_queue.i x cctools-4.3.2-source/work_queue/src/python3/work_queue_example.py x cctools-4.3.2-source/work_queue/src/sge_submit_workers x cctools-4.3.2-source/work_queue/src/slurm_submit_workers x cctools-4.3.2-source/work_queue/src/torque_submit_workers x cctools-4.3.2-source/work_queue/src/trickle.sh x cctools-4.3.2-source/work_queue/src/work_queue.c x cctools-4.3.2-source/work_queue/src/work_queue.h x cctools-4.3.2-source/work_queue/src/work_queue.i x cctools-4.3.2-source/work_queue/src/work_queue_benchmark.sh x cctools-4.3.2-source/work_queue/src/work_queue_catalog.c x cctools-4.3.2-source/work_queue/src/work_queue_catalog.h x cctools-4.3.2-source/work_queue/src/work_queue_example.c x cctools-4.3.2-source/work_queue/src/work_queue_graph_log x cctools-4.3.2-source/work_queue/src/work_queue_internal.h x cctools-4.3.2-source/work_queue/src/work_queue_pool.c x cctools-4.3.2-source/work_queue/src/work_queue_pool.conf.example x cctools-4.3.2-source/work_queue/src/work_queue_priority_test.c x cctools-4.3.2-source/work_queue/src/work_queue_process.c x cctools-4.3.2-source/work_queue/src/work_queue_process.h x cctools-4.3.2-source/work_queue/src/work_queue_protocol.h x cctools-4.3.2-source/work_queue/src/work_queue_resources.c x cctools-4.3.2-source/work_queue/src/work_queue_resources.h x cctools-4.3.2-source/work_queue/src/work_queue_status.c x cctools-4.3.2-source/work_queue/src/work_queue_test.c x cctools-4.3.2-source/work_queue/src/work_queue_test_main.c x cctools-4.3.2-source/work_queue/src/work_queue_test_watch.c x cctools-4.3.2-source/work_queue/src/work_queue_watcher.c x cctools-4.3.2-source/work_queue/src/work_queue_watcher.h x cctools-4.3.2-source/work_queue/src/work_queue_worker.c x cctools-4.3.2-source/work_queue/src/wq_submit_workers.common x cctools-4.3.2-source/work_queue/test/ x cctools-4.3.2-source/work_queue/test/TR_work_queue_foreman.sh x cctools-4.3.2-source/work_queue/test/TR_work_queue_multicore.sh x cctools-4.3.2-source/work_queue/test/TR_work_queue_single.sh x cctools-4.3.2-source/work_queue/test/work_queue_common.sh tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/b/c/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/b/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/a/_acl) failed: No such file or directory tar: copyfile unpack (cctools-4.3.2-source/parrot/test/fixtures/_acl) failed: No such file or directory goliath:Downloads pivie$ ./configure Darwin Goliath.local 14.1.0 Darwin Kernel Version 14.1.0: Thu Feb 26 19:26:47 PST 2015; root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64 checking for package compatibility... parrot is NOT supported on DARWIN for any cpu type resource_monitor IS supported on DARWIN checking for multiarch environment...no checking for all the things I know how to build... package dttools found package makeflow found package work_queue found package sand found package allpairs found package wavefront found package ftp_lite found package resource_monitor found package resource_monitor_visualizer found package makeflow_linker found package chirp found package weaver found package doc found checking for gcc.../usr/bin/gcc checking for g++.../usr/bin/g++ checking for GNU make in several places... checking for make.../usr/bin/make checking if make is GNU make...yes checking if gcc supports -Wno-unused-parameter...yes checking if gcc supports -Wno-unknown-pragmas...yes checking if gcc supports -Wno-deprecated-declarations...yes checking if gcc supports -Wno-unused-const-variable...yes checking if ld supports the --as-needed flag...no using a globus flavor of 'gcc64' (if this is wrong, use the --globus-flavor argument) checking for /usr/include/gcc64/globus_common.h...no checking for /usr/include/globus/globus_common.h...no

dthain commented 9 years ago

@pivie @hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

pivie commented 9 years ago

I am sorry I haven't gotten to this yet. I was going to get a clean install of OS 10.10.2 and start from there, but I can try to suggest libraries that have a chance of helping.

Aurélien, do you use something like homebrew or macports to install packages, or do you usually install things directly?

On Fri, Mar 27, 2015 at 4:44 PM, Douglas Thain notifications@github.com wrote:

@pivie https://github.com/pivie @hmeng-19 https://github.com/hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie https://github.com/ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie https://github.com/pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-87084560 .

pivie commented 9 years ago

I found a machine that has the same problem. I have tried installing the homebrew packages the working one has that the other one doesn't, but no luck yet. I will try to compare environment variables and then it is back to google to figure out how I got it working in the first place.

On Fri, Mar 27, 2015 at 5:08 PM, Peter Ivie pivie@nd.edu wrote:

I am sorry I haven't gotten to this yet. I was going to get a clean install of OS 10.10.2 and start from there, but I can try to suggest libraries that have a chance of helping.

Aurélien, do you use something like homebrew or macports to install packages, or do you usually install things directly?

On Fri, Mar 27, 2015 at 4:44 PM, Douglas Thain notifications@github.com wrote:

@pivie https://github.com/pivie @hmeng-19 https://github.com/hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie https://github.com/ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie https://github.com/pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-87084560 .

pivie commented 9 years ago

Aurélien, do you have the same version of Xcode Command Line Tools that I have in the attached screenshot?

On Fri, Mar 27, 2015 at 6:11 PM, Peter Ivie pivie@nd.edu wrote:

I found a machine that has the same problem. I have tried installing the homebrew packages the working one has that the other one doesn't, but no luck yet. I will try to compare environment variables and then it is back to google to figure out how I got it working in the first place.

On Fri, Mar 27, 2015 at 5:08 PM, Peter Ivie pivie@nd.edu wrote:

I am sorry I haven't gotten to this yet. I was going to get a clean install of OS 10.10.2 and start from there, but I can try to suggest libraries that have a chance of helping.

Aurélien, do you use something like homebrew or macports to install packages, or do you usually install things directly?

On Fri, Mar 27, 2015 at 4:44 PM, Douglas Thain notifications@github.com wrote:

@pivie https://github.com/pivie @hmeng-19 https://github.com/hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie https://github.com/ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie https://github.com/pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-87084560 .

pivie commented 9 years ago

Two more questions about your setup: 1- Do you have a /usr/include/ directory? 2- What is the full output of 'gcc --version'?

On Fri, Mar 27, 2015 at 6:42 PM, Peter Ivie pivie@nd.edu wrote:

Aurélien, do you have the same version of Xcode Command Line Tools that I have in the attached screenshot?

On Fri, Mar 27, 2015 at 6:11 PM, Peter Ivie pivie@nd.edu wrote:

I found a machine that has the same problem. I have tried installing the homebrew packages the working one has that the other one doesn't, but no luck yet. I will try to compare environment variables and then it is back to google to figure out how I got it working in the first place.

On Fri, Mar 27, 2015 at 5:08 PM, Peter Ivie pivie@nd.edu wrote:

I am sorry I haven't gotten to this yet. I was going to get a clean install of OS 10.10.2 and start from there, but I can try to suggest libraries that have a chance of helping.

Aurélien, do you use something like homebrew or macports to install packages, or do you usually install things directly?

On Fri, Mar 27, 2015 at 4:44 PM, Douglas Thain <notifications@github.com

wrote:

@pivie https://github.com/pivie @hmeng-19 https://github.com/hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie https://github.com/ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie https://github.com/pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-87084560 .

pivie commented 9 years ago

Aurélien,

If you don't have a /usr/include/ directory, could you try running the following command? xcode-select --install

A window will pop up for you to install Xcode Command Line Tools. After this, the machine (that previously had your same error) compiled the cctools source code without a hitch.

There were a few other things I did, but I think this one is the one that made the difference. Let me know if that did or didn't solve your problem.

On Fri, Mar 27, 2015 at 8:28 PM, Peter Ivie pivie@nd.edu wrote:

Two more questions about your setup: 1- Do you have a /usr/include/ directory? 2- What is the full output of 'gcc --version'?

On Fri, Mar 27, 2015 at 6:42 PM, Peter Ivie pivie@nd.edu wrote:

Aurélien, do you have the same version of Xcode Command Line Tools that I have in the attached screenshot?

On Fri, Mar 27, 2015 at 6:11 PM, Peter Ivie pivie@nd.edu wrote:

I found a machine that has the same problem. I have tried installing the homebrew packages the working one has that the other one doesn't, but no luck yet. I will try to compare environment variables and then it is back to google to figure out how I got it working in the first place.

On Fri, Mar 27, 2015 at 5:08 PM, Peter Ivie pivie@nd.edu wrote:

I am sorry I haven't gotten to this yet. I was going to get a clean install of OS 10.10.2 and start from there, but I can try to suggest libraries that have a chance of helping.

Aurélien, do you use something like homebrew or macports to install packages, or do you usually install things directly?

On Fri, Mar 27, 2015 at 4:44 PM, Douglas Thain < notifications@github.com> wrote:

@pivie https://github.com/pivie @hmeng-19 https://github.com/hmeng-19 I think it is already understood that cctools builds on some machines, but it is not building on @ajmazurie https://github.com/ajmazurie 's machine. It is not helpful to show him that it builds on our machines. His error message clearly indicates that the problem is that /usr/include/getopt.h is not present on his machine.

@pivie https://github.com/pivie please figure out for us what package or option provides /usr/include/getopt.h on OSX.

— Reply to this email directly or view it on GitHub https://github.com/cooperative-computing-lab/cctools/issues/691#issuecomment-87084560 .

ajmazurie commented 9 years ago

@pivie Here are my answers to your questions:

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.1.0
Thread model: posix
ajmazurie commented 9 years ago

@pivie Success! By running xcode-select --install I got the following notice: "xcode-select: note: install requested for command line developer tools" and got a brand new /usr/include/ folder! I confirm that a /usr/include/getopt.h file is present. More importantly, I confirm that cctools now compiles correctly! The installation of the Xcode command line tools did the trick.

dthain commented 9 years ago

@pivie please add a note to our install instructions so that others can avoid this problem, thanks.

batrick commented 9 years ago

Resolved by #711.