[ExM Users] Problem Building exm v0.8.0 on Linux
Tim Armstrong
tim.g.armstrong at gmail.com
Tue Aug 11 15:01:22 CDT 2015
It looks like it's not pointed correctly at python - what Python settings
did you have enabled in your settings file?
- Tim
On 11 August 2015 at 12:43, Timothy Stitt (TGAC) <Timothy.Stitt at tgac.ac.uk>
wrote:
> Thanks Tim.
>
> I commented out the optimised build option and rebuilt. Unfortunately, it
> didn’t get any better. I’ve attached the full build log.
>
> I also ran 'make check_includes'. The output is as follows:
>
> [stittt at v0267] /tgac/software/testing/exm/0.8.0/src/turbine > make
> check_includes
> CHECK.SH
> Not found: python2.7/Python.h
> Not found: tests/staticapp-1.c
> Not found: tests/staticapp-bundled-1.c
>
> Cheers,
>
> 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
>
> From: Tim Armstrong <tim.g.armstrong at gmail.com>
> Date: Tuesday, 11 August 2015 18:04
> To: Timothy Stitt <timothy.stitt at tgac.ac.uk>
> Cc: "exm-user at lists.mcs.anl.gov" <exm-user at lists.mcs.anl.gov>
> Subject: Re: [ExM Users] Problem Building exm v0.8.0 on Linux
>
> 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_DEPSsrc/executables/turbine_sh.manifest.d
>> DEPsrc/tcl/static-pkg/static-pkg.d
>> MKSTATIC_DEPStests/staticapp-bundled-1.manifest.d
>> MKSTATIC_DEPStests/staticapp-1.manifest.d
>> TCLsrc/util/debug.h
>> MKSTATICsrc/executables/turbine_sh.c
>> DEPsrc/tcl/turbine/tcl-turbine.d
>> DEPsrc/tcl/adlb/tcl-adlb.d
>> DEPsrc/tcl/julia/tcl-julia.d
>> DEPsrc/util/debug.d
>> DEPsrc/turbine/executors/noop_executor.d
>> DEPsrc/turbine/async_exec.d
>> DEPsrc/turbine/worker.d
>> DEPsrc/turbine/cache.d
>> DEPsrc/turbine/turbine.d
>> DEPsrc/executables/turbine_sh.d
>> CCsrc/tcl/static-pkg/static-pkg.o
>> CCsrc/turbine/turbine.o
>> CCsrc/turbine/cache.o
>> CCsrc/turbine/worker.o
>> CCsrc/turbine/executors/noop_executor.o
>> CCsrc/turbine/async_exec.o
>> CCsrc/util/debug.o
>> CCsrc/tcl/julia/tcl-julia.o
>> CCsrc/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",
>> ^
>> ARlib/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
>>
>>
>
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