[ExM Users] Problem Building exm v0.8.0 on Linux
Timothy Stitt (TGAC)
Timothy.Stitt at tgac.ac.uk
Tue Aug 11 14:43:51 CDT 2015
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<mailto:timothy.stitt at tgac.ac.uk>
From: Tim Armstrong <tim.g.armstrong at gmail.com<mailto:tim.g.armstrong at gmail.com>>
Date: Tuesday, 11 August 2015 18:04
To: Timothy Stitt <timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>>
Cc: "exm-user at lists.mcs.anl.gov<mailto:exm-user at lists.mcs.anl.gov>" <exm-user at lists.mcs.anl.gov<mailto: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<mailto: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<http://module.mk>
config.status: creating src/util/module.mk<http://module.mk>
config.status: creating src/util/debug-tokens.tcl
config.status: creating src/tcl/module.mk<http://module.mk>
config.status: creating src/tcl/adlb/module.mk<http://module.mk>
config.status: creating src/tcl/blob/module.mk<http://module.mk>
config.status: creating src/tcl/c-utils/module.mk<http://module.mk>
config.status: creating src/tcl/mpe/module.mk<http://module.mk>
config.status: creating src/tcl/julia/module.mk<http://module.mk>
config.status: creating src/tcl/python/module.mk<http://module.mk>
config.status: creating src/tcl/r/module.mk<http://module.mk>
config.status: creating src/tcl/static-pkg/module.mk<http://module.mk>
config.status: creating src/tcl/turbine/module.mk<http://module.mk>
config.status: creating src/executables/module.mk<http://module.mk>
config.status: creating lib/module.mk<http://module.mk>
config.status: creating scripts/main-wrap/module.mk<http://module.mk>
config.status: creating scripts/submit/module.mk<http://module.mk>
config.status: creating scripts/submit/cobalt/module.mk<http://module.mk>
config.status: creating scripts/submit/cray/module.mk<http://module.mk>
config.status: creating scripts/submit/ec2/module.mk<http://module.mk>
config.status: creating scripts/submit/pbs/module.mk<http://module.mk>
config.status: creating scripts/submit/slurm/module.mk<http://module.mk>
config.status: creating scripts/turbine-config.sh
config.status: creating scripts/turbine-build-config.sh
config.status: creating tests/module.mk<http://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<http://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<http://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<tel:%2B44%201603%20450378>
e: timothy.stitt at tgac.ac.uk<mailto:timothy.stitt at tgac.ac.uk>
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