<div dir="ltr">Hi Tim,<div> 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.</div><div><br>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.</div><div><br></div><div>- Tim</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 11 August 2015 at 08:55, Timothy Stitt (TGAC) <span dir="ltr"><<a href="mailto:Timothy.Stitt@tgac.ac.uk" target="_blank">Timothy.Stitt@tgac.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
Dear support,</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
<br>
</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
I’ve been wrestling with building exm v0.8.0 on our RHEL 6.0 Linux system. I’m using gcc v4.9.1.</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
<br>
</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
When building the Turbine package it fails with the following:</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
<br>
</div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
<snip></div>
<div>
<div><font color="#183669" face="Candara,sans-serif">Preparing config files: please wait...</font></div>
<div><font color="#183669" face="Candara,sans-serif">configure: creating ./config.status</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/turbine/turbine-version.h</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/turbine/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/util/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/util/debug-tokens.tcl</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/adlb/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/blob/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/c-utils/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/mpe/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/julia/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/python/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/r/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/static-pkg/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/tcl/turbine/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating src/executables/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating lib/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/main-wrap/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/cobalt/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/cray/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/ec2/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/pbs/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/submit/slurm/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/turbine-config.sh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating scripts/turbine-build-config.sh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating tests/<a href="http://module.mk" target="_blank">module.mk</a></font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating tests/runbin.zsh</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating Makefile</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: creating config.h</font></div>
<div><font color="#183669" face="Candara,sans-serif">config.status: config.h is unchanged</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span style="white-space:pre-wrap">
</span>src/executables/turbine_sh.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/tcl/static-pkg/static-pkg.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span style="white-space:pre-wrap">
</span>tests/staticapp-bundled-1.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC_DEPS<span style="white-space:pre-wrap">
</span>tests/staticapp-1.manifest.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> TCL<span style="white-space:pre-wrap">
</span>src/util/debug.h</font></div>
<div><font color="#183669" face="Candara,sans-serif"> MKSTATIC<span style="white-space:pre-wrap">
</span>src/executables/turbine_sh.c</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/tcl/turbine/tcl-turbine.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/tcl/adlb/tcl-adlb.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/tcl/julia/tcl-julia.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/util/debug.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/turbine/executors/noop_executor.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/turbine/async_exec.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/turbine/worker.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/turbine/cache.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/turbine/turbine.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> DEP<span style="white-space:pre-wrap">
</span>src/executables/turbine_sh.d</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/tcl/static-pkg/static-pkg.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/turbine/turbine.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/turbine/cache.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/turbine/worker.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/turbine/executors/noop_executor.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/turbine/async_exec.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/util/debug.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/tcl/julia/tcl-julia.o</font></div>
<div><font color="#183669" face="Candara,sans-serif"> CC<span style="white-space:pre-wrap">
</span>src/tcl/adlb/tcl-adlb.o</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/executors/noop_executor.c: In function ‘noop_execute’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/executors/noop_executor.c:174:8: warning: variable ‘found_slot’ set but not used [-Wunused-but-set-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool found_slot = false;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/worker.c: In function ‘task_error’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/worker.c:102:7: warning: unused variable ‘rc’ [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "\n%s%s", prefix, command);</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c: In function ‘launch_error’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c:482:7: warning: unused variable ‘rc’ [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "Turbine %s worker task error in: %s",</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c: In function ‘callback_error’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/turbine/async_exec.c:501:7: warning: unused variable ‘rc’ [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc = asprintf(&msg, "Turbine %s worker task error in callback: %s",</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif"> AR<span style="white-space:pre-wrap">
</span>lib/libtclturbinestatic.a</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘adlb_setup_comm’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:384:7: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> int rc;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘tcl_dict_to_packed_container’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2132:1: warning: label ‘exit_err’ defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘tcl_list_to_packed_multiset’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2192:1: warning: label ‘exit_err’ defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘packed_struct_to_tcl_dict’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2247:17: warning: unused variable ‘name’ [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> const char *name = field_names[i];</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘get_compound_type’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5100:1: warning: label ‘exit_err’ defined but not used [-Wunused-label]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> exit_err:</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Subscript_Impl’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5645:11: warning: unused variable ‘sub’ [-Wunused-variable]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> char *sub = Tcl_GetStringFromObj(objv[i + 2], &sub_len);</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘adlb_datum2tclobj’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2707:22: warning: ‘tmp.value’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_datum_storage tmp;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:2739:17: warning: ‘tmp.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> *result = Tcl_NewStringObj(tmp.STRING.value,</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Enumerate_Cmd’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:3017:8: warning: ‘include_vals’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool include_vals;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:3016:8: warning: ‘include_keys’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> bool include_keys;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Refcount_Incr_Cmd’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4791:22: warning: ‘mode’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_refcount_type mode;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Parse_Subscript’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5498:15: warning: ‘tmp_sub.length’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> sub->length += to_append.length;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:5404:22: note: ‘tmp_sub.length’ was declared here</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_subscript tmp_sub;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c: In function ‘ADLB_Create_Nested_Impl.isra.52’:</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4340:8: warning: ‘retrieved.write_refs’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> if (retrieved.write_refs <= 0)</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">In file included from src/tcl/adlb/tcl-adlb.c:71:0:</font></div>
<div><font color="#183669" face="Candara,sans-serif">./src/tcl/util.h:164:5: warning: ‘<a href="http://retrieved.id" target="_blank">retrieved.id</a>’ may be used uninitialized in this function [-Wmaybe-uninitialized]</font></div>
<div><font color="#183669" face="Candara,sans-serif"> turbine_tcl_condition_failed(interp, objv[0], format, ## args); \</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">src/tcl/adlb/tcl-adlb.c:4333:14: note: ‘<a href="http://retrieved.id" target="_blank">retrieved.id</a>’ was declared here</font></div>
<div><font color="#183669" face="Candara,sans-serif"> adlb_ref retrieved;</font></div>
<div><font color="#183669" face="Candara,sans-serif"> ^</font></div>
<div><font color="#183669" face="Candara,sans-serif">exm-setup.zsh: turbine: build FAILED</font></div>
</div>
<div><font color="#183669" face="Candara,sans-serif"></snip></font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">I</font><font color="#183669" face="Candara,sans-serif"> see various warnings but no errors in the above</font><font color="#183669" face="Candara,sans-serif">…yet the setup fails. I would be grateful if
you could provide some assistance in diagnosing what is happening.</font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">Much appreciated,</font></div>
<div><font color="#183669" face="Candara,sans-serif"><br>
</font></div>
<div><font color="#183669" face="Candara,sans-serif">Tim.</font></div>
<div style="color:rgb(24,54,105);font-family:Candara,sans-serif;font-size:14px">
<p style="font-size:12px;margin:0px;font-family:Verdana">---</p>
<p style="margin:0px;font-family:Verdana"><span style="font-size:10px"><b>Timothy Stitt PhD</b> / Head of Scientific Computing</span></p>
<p style="margin:0px;font-family:Verdana"><span style="font-size:10px">The Genome Analysis Centre (TGAC), Room 204b</span></p>
<p style="margin:0px;font-family:Verdana;color:rgb(4,46,238)"><span style="text-decoration:underline;font-size:10px"><a href="http://www.tgac.ac.uk/" target="_blank">http://www.tgac.ac.uk/</a></span></p>
<p style="margin:0px;font-family:Cambria;min-height:19px"><span style="font-size:10px"><br>
</span></p>
<p style="margin:0px;font-family:Verdana"><span style="font-size:10px">p: <a href="tel:%2B44%201603%20450378" value="+441603450378" target="_blank">+44 1603 450378</a></span></p>
<p style="margin:0px;font-family:Verdana;color:rgb(13,102,213)"><span style="color:rgb(0,0,0);font-size:10px">e: <a href="mailto:timothy.stitt@tgac.ac.uk" target="_blank">timothy.stitt@tgac.ac.uk</a></span></p>
</div>
</div>
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