[ExM Users] Problem Building exm v0.8.0 on Linux
Tim Armstrong
tim.g.armstrong at gmail.com
Tue Aug 11 12:04:00 CDT 2015
Hi Tim,
There isn't an obvious smoking gun in there. If we had the full output to
see how far it got that might provide some hints.
I can suggest a couple of other things to try to dig down into the cause.
First, you could try running make check_includes in turbine/code - that
will report if a header is missing, which can cause a silent build failure.
Second, it looks like you're doing an optimised build - you could try doing
a non-optimised build and see if that succeeds.
- Tim
On 11 August 2015 at 08:55, Timothy Stitt (TGAC) <Timothy.Stitt at tgac.ac.uk>
wrote:
> Dear support,
>
> I’ve been wrestling with building exm v0.8.0 on our RHEL 6.0 Linux system.
> I’m using gcc v4.9.1.
>
> When building the Turbine package it fails with the following:
>
> <snip>
> Preparing config files: please wait...
> configure: creating ./config.status
> config.status: creating src/turbine/turbine-version.h
> config.status: creating src/turbine/module.mk
> config.status: creating src/util/module.mk
> config.status: creating src/util/debug-tokens.tcl
> config.status: creating src/tcl/module.mk
> config.status: creating src/tcl/adlb/module.mk
> config.status: creating src/tcl/blob/module.mk
> config.status: creating src/tcl/c-utils/module.mk
> config.status: creating src/tcl/mpe/module.mk
> config.status: creating src/tcl/julia/module.mk
> config.status: creating src/tcl/python/module.mk
> config.status: creating src/tcl/r/module.mk
> config.status: creating src/tcl/static-pkg/module.mk
> config.status: creating src/tcl/turbine/module.mk
> config.status: creating src/executables/module.mk
> config.status: creating lib/module.mk
> config.status: creating scripts/main-wrap/module.mk
> config.status: creating scripts/submit/module.mk
> config.status: creating scripts/submit/cobalt/module.mk
> config.status: creating scripts/submit/cray/module.mk
> config.status: creating scripts/submit/ec2/module.mk
> config.status: creating scripts/submit/pbs/module.mk
> config.status: creating scripts/submit/slurm/module.mk
> config.status: creating scripts/turbine-config.sh
> config.status: creating scripts/turbine-build-config.sh
> config.status: creating tests/module.mk
> config.status: creating tests/runbin.zsh
> config.status: creating Makefile
> config.status: creating config.h
> config.status: config.h is unchanged
> MKSTATIC_DEPS src/executables/turbine_sh.manifest.d
> DEP src/tcl/static-pkg/static-pkg.d
> MKSTATIC_DEPS tests/staticapp-bundled-1.manifest.d
> MKSTATIC_DEPS tests/staticapp-1.manifest.d
> TCL src/util/debug.h
> MKSTATIC src/executables/turbine_sh.c
> DEP src/tcl/turbine/tcl-turbine.d
> DEP src/tcl/adlb/tcl-adlb.d
> DEP src/tcl/julia/tcl-julia.d
> DEP src/util/debug.d
> DEP src/turbine/executors/noop_executor.d
> DEP src/turbine/async_exec.d
> DEP src/turbine/worker.d
> DEP src/turbine/cache.d
> DEP src/turbine/turbine.d
> DEP src/executables/turbine_sh.d
> CC src/tcl/static-pkg/static-pkg.o
> CC src/turbine/turbine.o
> CC src/turbine/cache.o
> CC src/turbine/worker.o
> CC src/turbine/executors/noop_executor.o
> CC src/turbine/async_exec.o
> CC src/util/debug.o
> CC src/tcl/julia/tcl-julia.o
> CC src/tcl/adlb/tcl-adlb.o
> src/turbine/executors/noop_executor.c: In function ‘noop_execute’:
> src/turbine/executors/noop_executor.c:174:8: warning: variable
> ‘found_slot’ set but not used [-Wunused-but-set-variable]
> bool found_slot = false;
> ^
> src/turbine/worker.c: In function ‘task_error’:
> src/turbine/worker.c:102:7: warning: unused variable ‘rc’
> [-Wunused-variable]
> int rc = asprintf(&msg, "\n%s%s", prefix, command);
> ^
> src/turbine/async_exec.c: In function ‘launch_error’:
> src/turbine/async_exec.c:482:7: warning: unused variable ‘rc’
> [-Wunused-variable]
> int rc = asprintf(&msg, "Turbine %s worker task error in: %s",
> ^
> src/turbine/async_exec.c: In function ‘callback_error’:
> src/turbine/async_exec.c:501:7: warning: unused variable ‘rc’
> [-Wunused-variable]
> int rc = asprintf(&msg, "Turbine %s worker task error in callback: %s",
> ^
> AR lib/libtclturbinestatic.a
> src/tcl/adlb/tcl-adlb.c: In function ‘adlb_setup_comm’:
> src/tcl/adlb/tcl-adlb.c:384:7: warning: variable ‘rc’ set but not used
> [-Wunused-but-set-variable]
> int rc;
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘tcl_dict_to_packed_container’:
> src/tcl/adlb/tcl-adlb.c:2132:1: warning: label ‘exit_err’ defined but not
> used [-Wunused-label]
> exit_err:
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘tcl_list_to_packed_multiset’:
> src/tcl/adlb/tcl-adlb.c:2192:1: warning: label ‘exit_err’ defined but not
> used [-Wunused-label]
> exit_err:
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘packed_struct_to_tcl_dict’:
> src/tcl/adlb/tcl-adlb.c:2247:17: warning: unused variable ‘name’
> [-Wunused-variable]
> const char *name = field_names[i];
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘get_compound_type’:
> src/tcl/adlb/tcl-adlb.c:5100:1: warning: label ‘exit_err’ defined but not
> used [-Wunused-label]
> exit_err:
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Subscript_Impl’:
> src/tcl/adlb/tcl-adlb.c:5645:11: warning: unused variable ‘sub’
> [-Wunused-variable]
> char *sub = Tcl_GetStringFromObj(objv[i + 2], &sub_len);
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘adlb_datum2tclobj’:
> src/tcl/adlb/tcl-adlb.c:2707:22: warning: ‘tmp.value’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> adlb_datum_storage tmp;
> ^
> src/tcl/adlb/tcl-adlb.c:2739:17: warning: ‘tmp.length’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> *result = Tcl_NewStringObj(tmp.STRING.value,
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Enumerate_Cmd’:
> src/tcl/adlb/tcl-adlb.c:3017:8: warning: ‘include_vals’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> bool include_vals;
> ^
> src/tcl/adlb/tcl-adlb.c:3016:8: warning: ‘include_keys’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> bool include_keys;
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Refcount_Incr_Cmd’:
> src/tcl/adlb/tcl-adlb.c:4791:22: warning: ‘mode’ may be used uninitialized
> in this function [-Wmaybe-uninitialized]
> adlb_refcount_type mode;
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Parse_Subscript’:
> src/tcl/adlb/tcl-adlb.c:5498:15: warning: ‘tmp_sub.length’ may be used
> uninitialized in this function [-Wmaybe-uninitialized]
> sub->length += to_append.length;
> ^
> src/tcl/adlb/tcl-adlb.c:5404:22: note: ‘tmp_sub.length’ was declared here
> adlb_subscript tmp_sub;
> ^
> src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Create_Nested_Impl.isra.52’:
> src/tcl/adlb/tcl-adlb.c:4340:8: warning: ‘retrieved.write_refs’ may be
> used uninitialized in this function [-Wmaybe-uninitialized]
> if (retrieved.write_refs <= 0)
> ^
> In file included from src/tcl/adlb/tcl-adlb.c:71:0:
> ./src/tcl/util.h:164:5: warning: ‘retrieved.id’ may be used uninitialized
> in this function [-Wmaybe-uninitialized]
> turbine_tcl_condition_failed(interp, objv[0], format, ## args); \
> ^
> src/tcl/adlb/tcl-adlb.c:4333:14: note: ‘retrieved.id’ was declared here
> adlb_ref retrieved;
> ^
> exm-setup.zsh: turbine: build FAILED
> </snip>
>
> I see various warnings but no errors in the above…yet the setup fails. I
> would be grateful if you could provide some assistance in diagnosing what
> is happening.
>
> Much appreciated,
>
> Tim.
>
> ---
>
> *Timothy Stitt PhD* / Head of Scientific Computing
>
> The Genome Analysis Centre (TGAC), Room 204b
>
> http://www.tgac.ac.uk/
>
>
> p: +44 1603 450378
>
> e: timothy.stitt at tgac.ac.uk
>
> _______________________________________________
> ExM-user mailing list
> ExM-user at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/exm-user
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/exm-user/attachments/20150811/75cda2ad/attachment-0001.html>
More information about the ExM-user
mailing list