<div dir="ltr">Markus<div><br></div><div>I have seen the "make" error on occasion here also. It works fine if I force a build so I agree with the race conditions analysis. However, do we have to drop to 1 when 2 or even 3 may have the same end result and not delay the builds as much. Either way we should may the default 1 and then we can use which ever value works best at each site.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, May 27, 2015 at 8:28 AM, <span dir="ltr"><<a href="mailto:markus.gerstel@diamond.ac.uk" target="_blank">markus.gerstel@diamond.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">We have recently seen intermittent build failures with the bootstrap base installation at Diamond. These all occurred during the compilation of python and were usually of the form<u></u><u></u></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Wl,-rpath=\$ORIGIN/../lib Parser/acceler.o Parser/grammar1.o
Parser/listnode.o Parser/node.o Parser/parser.o Parser/parsetok.o Parser/bitset.o Parser/metagrammar.o Parser/firstsets.o Parser/grammar.o Parser/pgen.o Objects/obmalloc.o Python/mysnprintf.o Python/pyctype.o Parser/tokenizer_pgen.o Parser/printgrammar.o Parser/pgenmain.o
-lpthread -ldl -lutil -o Parser/pgen<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: Parser/node.o: file not recognized: File truncated<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: collect2: ld returned 1 exit status<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: make[1]: *** [Parser/pgen] Error 1<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: make[1]: Leaving directory `/scratch/jenkins_slave/workspace/dials_bootstrap_platforms/compilationtarget/native/label/dials-ws154/build_dials/base_tmp/Python-2.7.8_cci'<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: make: *** [Include/graminit.h] Error 2<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">: make: *** Waiting for unfinished jobs....<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">Traceback (most recent call last):<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 1194, in <module><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> installer(args=sys.argv, log=sys.stdout)<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 184, in __init__<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> self.build_dependencies(packages=packages)<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 571, in build_dependencies<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> getattr(self, 'build_%s'%i)()<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 622, in build_python<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> self.call('make -j %s install'%(self.nproc), log=log, cwd=python_dir)<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 264, in call<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> return call(args, log=log, verbose=self.verbose, **kwargs)<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> File "/scratch/jenkins_slave/workspace/dials_bootstrap_platforms/compilationtarget/native/label/dials-ws154/build_dials/modules/cctbx_project/libtbx/auto_build/installer_utils.py",
line 81, in call<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333"> raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Courier New";color:#333333">RuntimeError: Call to 'make -j 4 install' failed with exit code 2<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Other indicated errors are <u></u><u></u></p>
<p class="MsoNormal"> /usr/bin/ld: final link failed: File truncated<u></u><u></u></p>
<p class="MsoNormal">or<u></u><u></u></p>
<p class="MsoNormal">/usr/bin/ld: can not read symbols: File truncated<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I suspect that these errors are manifestations of a race condition in the python build process, which the bootstrap script now by default runs with a
<i>-j 4</i> parallel make. <u></u><u></u></p>
<p class="MsoNormal">To test this we are now using <i>--nproc=1</i> for the base installation step. We haven’t seen these build failures since.<u></u><u></u></p>
<p class="MsoNormal">I suggest we set the python compilation to never run with parallel make. Any other ideas?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">-Markus<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
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