[Distmake-general] distmake trying to link executable with out all dependencies
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[Distmake-general] distmake trying to link executable with out all dependencies
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From: Glen B. <Gle...@ja...> - 2009-12-17 15:00:44
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my Makefile works fine with make -j, however distmake is trying to link all the .o files without all of them being built. Occasionally it works correctly. For example, I see a message that it is building csv.o, but then later when it tries to build the executable it complains that csv.o odes not exist. It not always the same object file(s) that it can not find. Any ideas? gbeane@host> less submit_make.sh.o60580 === building 'all-recursive' in /home/gbeane/hmmSNP/dev on host 'cs-short-1' Making all in src distmake[1]: Entering directory `/home/gbeane/hmmSNP/dev/src' === building 'all-recursive' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' Making all in include distmake[2]: Entering directory `/home/gbeane/hmmSNP/dev/src/include' === building 'config.h' in /home/gbeane/hmmSNP/dev/src/include on host 'cs-short-1' distmake all-am === building 'all' in /home/gbeane/hmmSNP/dev/src/include on host 'cs-short-1' distmake[3]: Entering directory `/home/gbeane/hmmSNP/dev/src/include' === building 'config.h' in /home/gbeane/hmmSNP/dev/src/include on host 'cs-short-1' distmake[3]: Leaving directory `/home/gbeane/hmmSNP/dev/src/include' distmake[2]: Leaving directory `/home/gbeane/hmmSNP/dev/src/include' distmake[2]: Entering directory `/home/gbeane/hmmSNP/dev/src' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c === building 'main.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT dataIO.o -MD -MP -MF .deps/dataIO.Tpo -c -o dataIO.o dataIO.c === building 'dataIO.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT CLI.o -MD -MP -MF .deps/CLI.Tpo -c -o CLI.o CLI.c === building 'CLI.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT hmm_em.o -MD -MP -MF .deps/hmm_em.Tpo -c -o hmm_em.o hmm_em.c === building 'hmm_em.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT hmmMatrix.o -MD -MP -MF .deps/hmmMatrix.Tpo -c -o hmmMatrix.o hmmMatrix.c === building 'hmmMatrix.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT dataFilter.o -MD -MP -MF .deps/dataFilter.Tpo -c -o dataFilter.o dataFilter.c === building 'dataFilter.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT filter.o -MD -MP -MF .deps/filter.Tpo -c -o filter.o filter.c === building 'filter.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT path.o -MD -MP -MF .deps/path.Tpo -c -o path.o path.c === building 'path.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/dataFilter.Tpo .deps/dataFilter.Po === building 'dataFilter.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT fill.o -MD -MP -MF .deps/fill.Tpo -c -o fill.o fill.c === building 'fill.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/filter.Tpo .deps/filter.Po === building 'filter.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT graph.o -MD -MP -MF .deps/graph.Tpo -c -o graph.o graph.c === building 'graph.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/fill.Tpo .deps/fill.Po === building 'fill.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT prune.o -MD -MP -MF .deps/prune.Tpo -c -o prune.o prune.c === building 'prune.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/CLI.Tpo .deps/CLI.Po === building 'CLI.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT hmmUtil.o -MD -MP -MF .deps/hmmUtil.Tpo -c -o hmmUtil.o hmmUtil.c === building 'hmmUtil.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/main.Tpo .deps/main.Po === building 'main.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT rand.o -MD -MP -MF .deps/rand.Tpo -c -o rand.o rand.c === building 'rand.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/path.Tpo .deps/path.Po === building 'path.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT sort_max_trace.o -MD -MP -MF .deps/sort_max_trace.Tpo -c -o sort_max_trace.o sort_max_tra ce.c === building 'sort_max_trace.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/graph.Tpo .deps/graph.Po === building 'graph.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT csv.o -MD -MP -MF .deps/csv.Tpo -c -o csv.o csv.c === building 'csv.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/prune.Tpo .deps/prune.Po === building 'prune.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT temp_file_cleanup.o -MD -MP -MF .deps/temp_file_cleanup.Tpo -c -o temp_file_cleanup.o tem p_file_cleanup.c === building 'temp_file_cleanup.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-2' mv -f .deps/rand.Tpo .deps/rand.Po === building 'rand.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/hmmUtil.Tpo .deps/hmmUtil.Po === building 'hmmUtil.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/hmm_em.Tpo .deps/hmm_em.Po === building 'hmm_em.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -c ../src/version.c === building 'version.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -DHAVE_CONFIG_H -I. -I../src/include -I../src/include -std=gnu99 -Wall -pedantic -Werror -g -O2 -MT state_sorting.o -MD -MP -MF .deps/state_sorting.Tpo -c -o state_sorting.o state_sorting.c === building 'state_sorting.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/state_sorting.Tpo .deps/state_sorting.Po === building 'state_sorting.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/temp_file_cleanup.Tpo .deps/temp_file_cleanup.Po === building 'temp_file_cleanup.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/csv.Tpo .deps/csv.Po === building 'csv.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/hmmMatrix.Tpo .deps/hmmMatrix.Po === building 'hmmMatrix.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/sort_max_trace.Tpo .deps/sort_max_trace.Po === building 'sort_max_trace.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' mv -f .deps/dataIO.Tpo .deps/dataIO.Po === building 'dataIO.o' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' === building 'hmmSNP' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc -std=gnu99 -Wall -pedantic -Werror -g -O2 -o hmmSNP main.o dataIO.o CLI.o hmm_em.o hmmMatri x.o dataFilter.o filter.o path.o fill.o graph.o prune.o hmmUtil.o rand.o sort_max_trace.o csv.o te mp_file_cleanup.o version.o state_sorting.o -lm === building 'hmmSNP' in /home/gbeane/hmmSNP/dev/src on host 'cs-short-1' gcc: graph.o: No such file or directory gcc: prune.o: No such file or directory gcc: sort_max_trace.o: No such file or directory gcc: csv.o: No such file or directory gcc: temp_file_cleanup.o: No such file or directory distmake[2]: *** [hmmSNP] Error 1 distmake[2]: Leaving directory `/home/gbeane/hmmSNP/dev/src' distmake[1]: *** [all-recursive] Error 1 distmake[1]: Leaving directory `/home/gbeane/hmmSNP/dev/src' -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153 |