[ExM Users] Problem Building exm v0.8.0 on Linux

Tue Aug 11 10:55:43 CDT 2015

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<mailto:timothy.stitt at tgac.ac.uk>
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