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<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Dear Anshu,</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Thank you for the advice. </FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">This email contains two errors. One is the “gmake” error
when I type “ ./setup Sedov –auto +ug +noio”. The other is a “gmake warning”
when I type “./setup Sedov -auto”.</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><FONT
face="Times New Roman"><SPAN style="FONT-SIZE: 14pt" lang=EN-US>1. When I type
“./setup Sedov –auto +ug +noio”, there is a error comes out in the step of
gmake</SPAN><SPAN lang=EN-US><FONT size=3>. </FONT></SPAN></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">The following is the last part of the
error:</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/opt/software/mpich2-gnu/lib/libmpich.a(simple_pmi.o): In
function `PMI_Init':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">simple_pmi.c:(.text+0x<st1:chmetcnv TCSC="0"
NumberType="1" Negative="False" HasSpace="False" SourceValue="15" UnitName="C"
w:st="on">15c</st1:chmetcnv>0): warning: Using 'gethostbyname' in statically
linked applications requires at runtime the shared libraries from the glibc
version used for linking</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x247): undefined reference to
`pthread_getschedparam'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x384): undefined reference to
`pthread_cond_signal'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x421): undefined reference to
`pthread_attr_init'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x42e): undefined reference to
`pthread_attr_setdetachstate'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x43b): undefined reference to
`pthread_attr_setstacksize'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `__aio_enqueue_request':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x494): undefined reference to
`pthread_attr_destroy'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x660): undefined reference to
`pthread_getschedparam'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x694): undefined reference to
`pthread_setschedparam'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x820): undefined reference to
`pthread_cond_signal'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x8fd): undefined reference to
`pthread_attr_init'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x<st1:chmetcnv TCSC="0" NumberType="1"
Negative="False" HasSpace="False" SourceValue="90" UnitName="a"
w:st="on">90a</st1:chmetcnv>): undefined reference to
`pthread_attr_setdetachstate'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_misc.o): In
function `handle_fildes_io':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0x9dd): undefined reference to
`pthread_cond_timedwait'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_notify.o): In
function `__aio_notify_only':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0xb7): undefined reference to
`pthread_attr_init'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/usr/lib/gcc/x86_64-redhat-linux/<st1:chsdate w:st="on"
IsROCDate="False" IsLunarDate="False" Day="30" Month="12"
Year="1899">4.1.2</st1:chsdate>/../../../../lib64/librt.a(aio_notify.o): In
function `__aio_notify_only':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">(.text+0xc4): undefined reference to
`pthread_attr_setdetachstate'</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">collect2: ld returned 1 exit status</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">gmake: *** [flash3] Error 1</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN style="FONT-SIZE: 14pt"
lang=EN-US><FONT face="Times New Roman">I don’t know what
happens.<o:p></o:p></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN style="FONT-SIZE: 14pt"
lang=EN-US><FONT face="Times New Roman">2. When following the user’s guide, I
type “./setup Sedov -auto”. I see a “warning”, and I don’t know whether it is
ok.<o:p></o:p></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">The following is the “warning”:</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">/opt/hdf-<st1:chsdate w:st="on" IsROCDate="False"
IsLunarDate="False" Day="30" Month="12"
Year="1899">1.6.5</st1:chsdate>/lib/libhdf5.a(H5FDstream.o): In function
`H5FD_stream_open':</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">H5FDstream.c:(.text+0x1207): warning: Using
'gethostbyname' in statically linked applications requires at runtime the shared
libraries from the glibc version used for linking</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">SUCCESS</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Is it ok? I see “SUCCESS” in the last line.
</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">At last, I want to tell you some information about my
computer. It just has one computer, two Intel Xeon CPU. The system is CentOS
5.5. The version of MPI is mpich2-<st1:chsdate w:st="on" IsROCDate="False"
IsLunarDate="False" Day="30" Month="12" Year="1899">1.2.1</st1:chsdate>. The
version of gcc and gfortran is 4.1.2.</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><o:p><FONT
size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Best wishes,</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Zhang Chao</FONT></SPAN></P></FONT></DIV>
<DIV style="FONT: 10pt Tahoma">
<DIV><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=dubey@flash.uchicago.edu
href="mailto:dubey@flash.uchicago.edu">Anshu Dubey</A> </DIV>
<DIV><B>Sent:</B> Monday, June 20, 2011 11:19 AM</DIV>
<DIV><B>To:</B> <A title=walli1986@hotmail.com
href="mailto:walli1986@hotmail.com">Zhang Chao</A> </DIV>
<DIV><B>Cc:</B> <A title=flash-users@flash.uchicago.edu
href="mailto:flash-users@flash.uchicago.edu">flash-users@flash.uchicago.edu</A>
</DIV>
<DIV><B>Subject:</B> Re: [FLASH-USERS] The problem "Segmentation
fault"</DIV></DIV></DIV>
<DIV><BR></DIV>Dear Zhang,<BR><BR>Would you please try the following and let me
know what happens.<BR><BR>Modify your setup line to<BR>./setup Sedov -auto +ug
+noio<BR><BR>then build using gmake and try to run it.<BR><BR>Also, could you
tell us what are the versions of MPI, gfortran and gcc you are
running.<BR>Please make sure that your MPI library was built with the same
version of gcc that<BR>you are using to build FLASH.<BR><BR>Anshu<BR><BR>
<DIV class=gmail_quote>2011/6/19 Zhang Chao <SPAN dir=ltr><<A
href="mailto:walli1986@hotmail.com">walli1986@hotmail.com</A>></SPAN><BR>
<BLOCKQUOTE
style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex"
class=gmail_quote><U></U>
<DIV style="PADDING-LEFT: 10px; PADDING-RIGHT: 10px; PADDING-TOP: 15px"
name="Compose message area">
<DIV><FONT size=2>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Dear all, </FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><U></U><FONT
size=3 face="Times New Roman"></FONT><U></U></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Can anyone help me? I met the “Segmentation fault” when
I type “./flash<U></U>3”<U></U>.</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><U></U><FONT
size=3 face="Times New Roman"></FONT><U></U></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">[walli@localhost object]$ ./flash3<BR>Segmentation
fault</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><U></U><FONT
size=3 face="Times New Roman"></FONT><U></U></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><U></U><FONT
size=3 face="Times New Roman"></FONT><U></U></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">It is really a big problem for me. I want to find a
solution in the internet, but until now, I still cannot solve the
problem.</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><U></U><FONT
size=3 face="Times New Roman"></FONT><U></U></SPAN> </P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Best wishes,</FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt" class=MsoNormal><SPAN lang=EN-US><FONT size=3
face="Times New Roman">Zhang
Chao</FONT></SPAN></P></FONT></DIV></DIV></BLOCKQUOTE></DIV><BR><BR
clear=all><BR>--
<BR>**********************************************************************************************************<BR>Anshu
Dubey<BR>Associate Director and CS/Applications Group
Leader 5747 S. Ellis
Avenue 3rd Flr.<BR>Flash Center for Computational
Science
773 834 2999 (office)<BR>Fellow, Computation
Institute
312 420 0033 (mobile)<BR>University of Chicago and Argonne National
Laboratory 773 834 3230
(fax)<BR>**********************************************************************************************************<BR><BR></BODY></HTML>