Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 04/07/11 19:18, Brice Goglin wrote: > Christopher, it should work starting with trunk r3535. Looks good to me with hwloc-1.3a1r3537. :-) Thanks! Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk4SlVwACgkQO2KABBYQAh+o7gCfREGmCbd+agP8DGg03BWh983D aM0An0i+PxtgV//Q+x49JT2KdHE/9TBd =bfDl -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
All this should be fixed now, and the configure output is now clear (it doesn't change its mind about pci_init/cleanup or pci_lookup_name without any obvious reason anymore). FC7: checking for pci/pci.h... yes checking for pci_init in -lpci... no checking for pci_init in -lpci with -lz... yes checking for pci_lookup_name in -lpci... no checking for inet_ntoa in -lresolv... yes checking for pci_lookup_name in -lpci with -lresolv... yes RHEL5.6: checking for pci/pci.h... yes checking for pci_init in -lpci... yes checking for pci_lookup_name in -lpci... no checking for inet_ntoa in -lresolv... yes checking for pci_lookup_name in -lpci with -lresolv... yes RHEL5.3: checking for pci/pci.h... yes checking for pci_init in -lpci... yes checking for pci_lookup_name in -lpci... yes Christopher, it should work starting with trunk r3535. Brice Le 30/06/2011 07:50, Brice Goglin a écrit : > Le 29/06/2011 13:18, Brice Goglin a écrit : >> I don't think we finally fixed this. >> >> IIRC, we need either a way to bypass the cache, or always add -lresolv >> even if it's useless (or find another way to detect if lresolv is needed). > Redefining our own HWLOC_AC_CHECK_LIB_NO_CACHE looks possible. > > Otherwise, we could use something different from AC_CHECK_LIB for the > second check (AC_SEARCH_LIBS uses a different cache name). > Or even use AC_LINK_IFELSE/AC_TRY_LINK which never cache anything. > > Brice > > ___ > hwloc-devel mailing list > hwloc-de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/hwloc-devel
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
pciutils was re-based to 3.1.7 in RHEL5.6 at the request of some of our hardware partners, in order to add some new hardware support. That'd explain why I didn't hit it when I was testing previously, we were still on CentOS 5.4 and RHEL 5.5 then so obviously this dependency is new in RHEL 5.6. Wonder if they'd consider it a bug ? Apparently not. The only bug filed about it (that I have found) is BZ 646884, which reported that kudzu failed to build after the update. The response to that was, "add -lresolv" --Guy
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
On Jun 17, 2011, at 7:52 AM, Brice Goglin wrote: > Advice from colleagues: This is becoming too ugly, this is libpci's > fault, just always add -lz -lresolv and let the linker drop them later > if they're useless :) Then we (might/probably will) get linker warnings when building hwloc. I'll tinker and see if a newer autoconf fixes the problem (i.e., no caching), because it definitely didn't happen to me last night. -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Advice from colleagues: This is becoming too ugly, this is libpci's
fault, just always add -lz -lresolv and let the linker drop them later
if they're useless :)
Brice
Le 17/06/2011 10:04, Christopher Samuel a écrit :
> On 17/06/11 17:14, Brice Goglin wrote:
>
> > Is there anyway to tell autoconf to ignore/drop some cached results?
> > Resetting the value of ac_cv_lib_pci_pci_lookup_name may work but I
> > don't know if we can do that (if we can, we should do it for
> > pci_init/pci_cleanup vs -lz too).
>
> Good guess Brice! This patch to configure from that nightly
> snapshot gets it working again:
>
> --- configure.old 2011-06-17 11:01:25.0 +1000
> +++ configure 2011-06-17 17:59:23.0 +1000
> @@ -10321,6 +10321,7 @@
> if test "x$ac_cv_lib_resolv_inet_ntoa" = x""yes; then :
>{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for
> pci_lookup_name in -lpci" >&5
> $as_echo_n "checking for pci_lookup_name in -lpci... " >&6; }
> +unset ac_cv_lib_pci_pci_lookup_name
> if test "${ac_cv_lib_pci_pci_lookup_name+set}" = set; then :
>$as_echo_n "(cached) " >&6
> else
>
> thus:
>
> checking pci/pci.h usability... yes
> checking pci/pci.h presence... yes
> checking for pci/pci.h... yes
> checking for pci_init in -lpci... yes
> checking for pci_lookup_name in -lpci... no
> checking for inet_ntoa in -lresolv... yes
> checking for pci_lookup_name in -lpci... yes
> checking whether PCI_LOOKUP_NO_NUMBERS is declared... yes
> checking for pci_find_cap in -lpci... yes
> checking whether struct pci_dev has a device_class field... yes
> checking whether struct pci_dev has a domain field... yes
>
> and it compiles and builds an lstopo which includes PCI info!
>
> cheers,
> Chris
___
hwloc-devel mailing list
hwloc-de...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/hwloc-devel
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 17/06/11 17:14, Brice Goglin wrote:
> Is there anyway to tell autoconf to ignore/drop some cached results?
> Resetting the value of ac_cv_lib_pci_pci_lookup_name may work but I
> don't know if we can do that (if we can, we should do it for
> pci_init/pci_cleanup vs -lz too).
Good guess Brice! This patch to configure from that nightly
snapshot gets it working again:
- --- configure.old 2011-06-17 11:01:25.0 +1000
+++ configure 2011-06-17 17:59:23.0 +1000
@@ -10321,6 +10321,7 @@
if test "x$ac_cv_lib_resolv_inet_ntoa" = x""yes; then :
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for pci_lookup_name in
-lpci" >&5
$as_echo_n "checking for pci_lookup_name in -lpci... " >&6; }
+unset ac_cv_lib_pci_pci_lookup_name
if test "${ac_cv_lib_pci_pci_lookup_name+set}" = set; then :
$as_echo_n "(cached) " >&6
else
thus:
checking pci/pci.h usability... yes
checking pci/pci.h presence... yes
checking for pci/pci.h... yes
checking for pci_init in -lpci... yes
checking for pci_lookup_name in -lpci... no
checking for inet_ntoa in -lresolv... yes
checking for pci_lookup_name in -lpci... yes
checking whether PCI_LOOKUP_NO_NUMBERS is declared... yes
checking for pci_find_cap in -lpci... yes
checking whether struct pci_dev has a device_class field... yes
checking whether struct pci_dev has a domain field... yes
and it compiles and builds an lstopo which includes PCI info!
cheers,
Chris
- --
Christopher Samuel - Senior Systems Administrator
VLSCI - Victorian Life Sciences Computation Initiative
Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545
http://www.vlsci.unimelb.edu.au/
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Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Le 17/06/2011 08:40, Christopher Samuel a écrit : > On 17/06/11 05:32, Jeff Squyres wrote: > > > Ok, good. I'll see if I can code this up. > > > ...done. Try a nightly trunk tarball >=r3516 > > (new nightly should be made in about 6 hours). > > Hmm, now it looks like it doesn't correctly enable > pci support.. > > checking pci/pci.h usability... yes > checking pci/pci.h presence... yes > checking for pci/pci.h... yes > checking for pci_init in -lpci... yes > checking for pci_lookup_name in -lpci... no > checking for inet_ntoa in -lresolv... yes > checking for pci_lookup_name in -lpci... (cached) no The problem is that it's cached so the first failure to find pci_lookup_name causes the second check to be bypassed. When fixing similar -lz problems, I had to look for another libpci symbol (pci_cleanup instead of pci_init) to prevent such caching problems. It makes the configure output strange because it may say that pci_init isn't available, add -lz and then say that pci_cleanup is available. Anyway, pci_lookup_name seems to be the only API function that ends up using the resolv code, so I don't see which other symbol to check for. Is there anyway to tell autoconf to ignore/drop some cached results? Resetting the value of ac_cv_lib_pci_pci_lookup_name may work but I don't know if we can do that (if we can, we should do it for pci_init/pci_cleanup vs -lz too). Brice
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 14/06/11 00:17, Jeff Squyres wrote: > Heh; next time you might want to compress. :-) Er, I think I forgot - it was late here.. ;-) > I got the logs; I'm looking at them now... Cool. > Are you sure that the config.log you sent matches > the makelog.txt? I see PCI checks in the configure > stdout, but nothing about that in config.log... Sigh, I think I ended up building in two different locations somehow - as I said, it was late. :-) I'll fix that up and send it on again.. Mea culpa, mea maxima culpa.. :-) - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32pnMACgkQO2KABBYQAh9j1ACeLrgNt6lW24VczVo353uzjVgC nG8An2yqoidfk7RJ4K2+WGC9qtpBXtS4 =ww6d -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Le 13/06/2011 22:38, Samuel Thibault a écrit : > Hello, > > Christopher Samuel, le Sun 12 Jun 2011 07:45:48 +0200, a écrit : >>> I fail to see how that symbol can ever get into >>> libhwloc.so, as we don't do any network thing at all... >> I *suspect* it's being pulled in by libpci - here: >> >> $ nm /usr/lib/libpci.a | grep res_query >> U __res_query > That's possible. And libpci does not announce this dependency in its > /usr/lib/pkgconfig/libpci.pc. I'm however surprised: don't you have a > /usr/lib/libpci.so which the hwloc link should be using instead of > libpci.a? libpci didn't ship a .so nor a .pc in the past. That's why we already have this mess about -lz in the configure. Brice
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Hello, Christopher Samuel, le Sun 12 Jun 2011 07:45:48 +0200, a écrit : > > I fail to see how that symbol can ever get into > > libhwloc.so, as we don't do any network thing at all... > > I *suspect* it's being pulled in by libpci - here: > > $ nm /usr/lib/libpci.a | grep res_query > U __res_query That's possible. And libpci does not announce this dependency in its /usr/lib/pkgconfig/libpci.pc. I'm however surprised: don't you have a /usr/lib/libpci.so which the hwloc link should be using instead of libpci.a? Samuel
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Heh; next time you might want to compress. :-) I got the logs; I'm looking at them now... Are you sure that the config.log you sent matches the makelog.txt? I see PCI checks in the configure stdout, but nothing about that in config.log... On Jun 13, 2011, at 9:28 AM, Christopher Samuel wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > On 13/06/11 23:11, Jeff Squyres wrote: > >> Chris -- could you send your config.log? > > Posted but currently held for moderation due to size.. > > - -- >Christopher Samuel - Senior Systems Administrator > VLSCI - Victorian Life Sciences Computation Initiative > Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 > http://www.vlsci.unimelb.edu.au/ > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAk32EJEACgkQO2KABBYQAh+N1ACfY2gTSkhf98S/h5wp5L8J6TbF > oAUAn05HwjFQ/B1AEsd5/lUGubHzqjO8 > =aSC4 > -END PGP SIGNATURE- > ___ > hwloc-devel mailing list > hwloc-de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/hwloc-devel -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/06/11 23:11, Jeff Squyres wrote: > Chris -- could you send your config.log? Posted but currently held for moderation due to size.. - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32EJEACgkQO2KABBYQAh+N1ACfY2gTSkhf98S/h5wp5L8J6TbF oAUAn05HwjFQ/B1AEsd5/lUGubHzqjO8 =aSC4 -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/06/11 23:11, Jeff Squyres wrote: > Chris -- could you send your config.log? Sure - attached to this email, along with a "makelog" which contains the output of configure && make V=1. > I'd like to see how it's deciding that libpci is ok > in configure if we cannot possibly ever link properly... I suspect that this symbol is getting pulled in only when it is being incorporated into the shared library, or perhaps when pci_lookup_name() is being called ? cheers! Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32Dy8ACgkQO2KABBYQAh+AwACfdy8HVEbv+LRKQ6lJ3W/ebmZA 9H4AnRkoR+HTFpW6hsL9KgbQJNFLOy6l =6Syz -END PGP SIGNATURE- This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by hwloc configure 1.3a1, which was generated by GNU Autoconf 2.65. Invocation command line was $ ./configure ## - ## ## Platform. ## ## - ## hostname = bruce-m.vlsci.unimelb.edu.au uname -m = x86_64 uname -r = 2.6.18-238.5.1.el5 uname -s = Linux uname -v = #1 SMP Fri Apr 1 18:41:58 EDT 2011 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/kerberos/sbin PATH: /usr/kerberos/bin PATH: /usr/local/sbin PATH: /usr/local/bin PATH: /sbin PATH: /bin PATH: /usr/sbin PATH: /usr/bin PATH: /opt/xcat/bin PATH: /opt/xcat/sbin PATH: /root/bin ## --- ## ## Core tests. ## ## --- ## configure:2841: checking build system type configure:2855: result: x86_64-unknown-linux-gnu configure:2875: checking host system type configure:2888: result: x86_64-unknown-linux-gnu configure:2908: checking target system type configure:2921: result: x86_64-unknown-linux-gnu configure:2965: checking for a BSD-compatible install configure:3033: result: /usr/bin/install -c configure:3044: checking whether build environment is sane configure:3094: result: yes configure:3235: checking for a thread-safe mkdir -p configure:3274: result: /bin/mkdir -p configure:3287: checking for gawk configure:3303: found /bin/gawk configure:3314: result: gawk configure:3325: checking whether make sets $(MAKE) configure:3347: result: yes configure:3422: checking how to create a ustar tar archive configure:3435: tar --version tar (GNU tar) 1.15.1 configure:3438: $? = 0 configure:3478: tardir=conftest.dir && eval tar --format=ustar -chf - "$tardir" >conftest.tar configure:3481: $? = 0 configure:3485: tar -xf - &5 gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50) Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:3914: $? = 0 configure:3903: gcc -v >&5 Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --disable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux Thread model: posix gcc version 4.1.2 20080704 (Red Hat 4.1.2-50) configure:3914: $? = 0 configure:3903: gcc -V >&5 gcc: '-V' option must have argument configure:3914: $? = 1 configure:3903: gcc -qversion >&5 gcc: unrecognized option '-qversion' gcc: no input files configure:3914: $? = 1 configure:3934: checking whether the C compiler works configure:3956: gccconftest.c >&5 configure:3960: $? = 0 configure:4009: result: yes configure:4012: checking for C compiler default output file name configure:4014: result: a.out configure:4020: checking for suffix of executables configure:4027: gcc -o conftestconftest.c >&5 configure:4031: $? = 0 configure:4053: result: configure:4075: checking whether we are cross compiling configure:4083: gcc -o conftestconftest.c >&5 configure:4087: $? = 0 configure:4094: ./conftest configure:4098: $? = 0 configure:4113: result: no configure:4118: checking for suffix of object files configure:4140: gcc -c conftest.c >&5 configure:4144: $? = 0 configure:4165: result: o configure:4169: checking whether we are using the GNU C compiler configure:4188: gcc -c conftest.c >&5 configure:4188: $? = 0
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Le 13/06/2011 14:45, Jeff Squyres a écrit : > Ah, that might explain it, then. > > I guess this means we need to add a few configure tests to figure out the dependencies of libpci (if any). Yuck. > > Do we have any idea what function in libpci is calling the resolver functionality? If you pass PCI_LOOKUP_NETWORK to the name-lookup functions (we don't), pci_id_net_lookup() gets called and it does a DNS-like resolving. No idea how it works. Brice
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/06/11 22:45, Jeff Squyres wrote: > Ah, that might explain it, then. Yeah.. :-( > I guess this means we need to add a few configure tests > to figure out the dependencies of libpci (if any). Yuck. Indeed. > Do we have any idea what function in libpci is calling the resolver > functionality? Complete guesswork from nm -l /usr/lib64/libpci.a, this is the object module where __res_query() is referenced: names-net.o: r .LC0 000b r .LC1 0072 r .LC10 r .LC11 0087 r .LC12 0030 r .LC13 0010 r .LC2 001a r .LC3 002e r .LC4 003a r .LC5 0041 r .LC6 004d r .LC7 005e r .LC8 0064 r .LC9 U _GLOBAL_OFFSET_TABLE_ U __h_errno_location U __memcpy_chk U __res_init U __res_query U __sprintf_chk U __stack_chk_fail U __strdup t dns_skip_name U pci_get_param 0060 T pci_id_net_lookup b resolver_inited.6042 Now that defines pci_id_net_lookup, and that appears to be referenced here: names.o: r .LC0 0003 r .LC1 0028 r .LC10 004f r .LC11 0054 r .LC12 005b r .LC13 0062 r .LC14 006c r .LC15 007b r .LC16 0081 r .LC17 0086 r .LC18 008c r .LC19 000e r .LC2 0092 r .LC20 0098 r .LC21 009e r .LC22 00a6 r .LC23 00b1 r .LC24 001a r .LC3 0029 r .LC4 002f r .LC5 0039 r .LC6 r .LC7 0046 r .LC8 004e r .LC9 U _GLOBAL_OFFSET_TABLE_ U __snprintf_chk U __sprintf_chk U __stack_chk_fail 0160 t format_name t format_name_pair 0250 t id_lookup 0380 t id_lookup_subsys U pci_id_cache_dirty U pci_id_cache_load U pci_id_insert U pci_id_lookup U pci_id_net_lookup U pci_load_name_list 0460 T pci_lookup_name U pci_mfree U snprintf That defines pci_lookup_name() and that is called from hwloc here: $ grep -R pci_lookup_name . ./src/topology-libpci.c:/* starting from pciutils 2.2, pci_lookup_name() takes a variable number ./src/topology-libpci.c:resname = pci_lookup_name(pciaccess, name, sizeof(name), ./src/topology-libpci.c:resname = pci_lookup_name(pciaccess, name, sizeof(name), ./src/topology-libpci.c:resname = pci_lookup_name(pciaccess, name, sizeof(name), So my guess it's the fact that we only have a static library that's causing the linker to pull in all the symbols, whether needed or not. :-( cheers! Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32CgcACgkQO2KABBYQAh+0/wCgkb10IWRnNxh5BicSrv6HC0U/ TIQAn2hmylDYzNx7Z8+oeR//zPtLRP3k =vhQT -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Ah, that might explain it, then. I guess this means we need to add a few configure tests to figure out the dependencies of libpci (if any). Yuck. Do we have any idea what function in libpci is calling the resolver functionality? On Jun 13, 2011, at 8:42 AM, Christopher Samuel wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > On 13/06/11 22:22, Jeff Squyres wrote: > >> Chris -- does nm on your libpci not show this? > > Nope, there is no libpci.so* on RHEL5.6, just a libpci.a. > > (and no, I've no idea why either!) > > cheers! > Chris > - -- >Christopher Samuel - Senior Systems Administrator > VLSCI - Victorian Life Sciences Computation Initiative > Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 > http://www.vlsci.unimelb.edu.au/ > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.11 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iEYEARECAAYFAk32BZ0ACgkQO2KABBYQAh9efQCfVMelwpuJr3s+IQYAAvr4QZmi > +soAoJg4UtDiAknoHK7oheHaQRgWSjvk > =ZHvx > -END PGP SIGNATURE- > ___ > hwloc-devel mailing list > hwloc-de...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/hwloc-devel -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/06/11 22:22, Jeff Squyres wrote: > Chris -- does nm on your libpci not show this? Nope, there is no libpci.so* on RHEL5.6, just a libpci.a. (and no, I've no idea why either!) cheers! Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32BZ0ACgkQO2KABBYQAh9efQCfVMelwpuJr3s+IQYAAvr4QZmi +soAoJg4UtDiAknoHK7oheHaQRgWSjvk =ZHvx -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13/06/11 19:41, Brice Goglin wrote: > libpci needs -lz in some cases, maybe it needs more. > However, in the case of -lz, we failed to configure > if we didn't add -lz to AC_CHECK_LIB. Your configure > works fine, right? Yup, configure works just fine and does add -lz. Very odd! cheers, Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk32BP4ACgkQO2KABBYQAh9BdwCggTP7Uy3G8n40WbUSUt8cs5UT XesAmgI4P8LI/LVwY01bBDMIHE2heriS =SIhh -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Le 13/06/2011 11:11, Christopher Samuel a écrit : > On 12/06/11 15:45, Christopher Samuel wrote: > > > I *suspect* it's being pulled in by libpci - here: > > > $ nm /usr/lib/libpci.a | grep res_query > > U __res_query Hello Chris, libpci needs -lz in some cases, maybe it needs more. However, in the case of -lz, we failed to configure if we didn't add -lz to AC_CHECK_LIB. Your configure works fine, right? Brice
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/06/11 15:45, Christopher Samuel wrote: > I *suspect* it's being pulled in by libpci - here: > > $ nm /usr/lib/libpci.a | grep res_query > U __res_query OK, looks like libpci may well be the culprit. Linking with the default libtool command line includes the symbol: $ /bin/sh ../libtool --tag=CC --mode=link gcc -g -fvisibility=hidden -I/usr/include/libxml2 -fvisibility=hidden -I/usr/include/libxml2 -I/tmp/HWLOC/hwloc-1.3a1r3511/include-no-undefined -version-number 0:0:0 -lxml2 -lz -lm-lpci -o libhwloc.la -rpath /usr/local/lib topology.lo traversal.lo distances.lo topology-synthetic.lo bind.lo cpuset.lo misc.lo topology-xml.lo topology-libpci.lo topology-linux.lo topology-x86.lo libtool: link: rm -fr .libs/libhwloc.la .libs/libhwloc.lai .libs/libhwloc.so .libs/libhwloc.so.0 .libs/libhwloc.so.0.0.0 libtool: link: gcc -g -shared .libs/topology.o .libs/traversal.o .libs/distances.o .libs/topology-synthetic.o .libs/bind.o .libs/cpuset.o .libs/misc.o .libs/topology-xml.o .libs/topology-libpci.o .libs/topology-linux.o .libs/topology-x86.o -lxml2 -lz -lm -lpci - -Wl,-soname -Wl,libhwloc.so.0 -o .libs/libhwloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libhwloc.so.0" && ln -s "libhwloc.so.0.0.0" "libhwloc.so.0") libtool: link: (cd ".libs" && rm -f "libhwloc.so" && ln -s "libhwloc.so.0.0.0" "libhwloc.so") libtool: link: ( cd ".libs" && rm -f "libhwloc.la" && ln -s "../libhwloc.la" "libhwloc.la" ) $ grep -R __res_query . Binary file ./.libs/libhwloc.so matches Binary file ./.libs/libhwloc.so.0.0.0 matches Binary file ./.libs/libhwloc.so.0 matches Removing the -lpci results in a library which no longer references it.. $ /bin/sh ../libtool --tag=CC --mode=link gcc -g -fvisibility=hidden -I/usr/include/libxml2 -fvisibility=hidden -I/usr/include/libxml2 -I/tmp/HWLOC/hwloc-1.3a1r3511/include-no-undefined -version-number 0:0:0 -lxml2 -lz -lm -o libhwloc.la -rpath /usr/local/lib topology.lo traversal.lo distances.lo topology-synthetic.lo bind.lo cpuset.lo misc.lo topology-xml.lo topology-libpci.lo topology-linux.lo topology-x86.lo libtool: link: rm -fr .libs/libhwloc.la .libs/libhwloc.lai .libs/libhwloc.so .libs/libhwloc.so.0 .libs/libhwloc.so.0.0.0 libtool: link: gcc -g -shared .libs/topology.o .libs/traversal.o .libs/distances.o .libs/topology-synthetic.o .libs/bind.o .libs/cpuset.o .libs/misc.o .libs/topology-xml.o .libs/topology-libpci.o .libs/topology-linux.o .libs/topology-x86.o -lxml2 -lz -lm - -Wl,-soname -Wl,libhwloc.so.0 -o .libs/libhwloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libhwloc.so.0" && ln -s "libhwloc.so.0.0.0" "libhwloc.so.0") libtool: link: (cd ".libs" && rm -f "libhwloc.so" && ln -s "libhwloc.so.0.0.0" "libhwloc.so") libtool: link: ( cd ".libs" && rm -f "libhwloc.la" && ln -s "../libhwloc.la" "libhwloc.la" ) $ grep -R __res_query . $ So it's a system library issue - over to you folks! :-) cheers, Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk311F4ACgkQO2KABBYQAh/iIgCffHbQkshfPPBOo+ls2JwXB2pO jSgAnjZqBtDsHZBJNVkmrxq6uJ9KRonv =ZC4K -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/06/11 11:42, Christopher Samuel wrote: > CCLD lstopo > /tmp/hwloc-1.3a1r3511/src/.libs/libhwloc.so: undefined reference to > `__res_query' For the record this happens with system GCC & GCC 4.4, Intel compilers and PGI compilers on RHEL 5.6 and CentOS 5.6 (both on our SGI CentOS system and a CentOS box run by another HPC center). I've even tried with ld from binutils 2.20.1 which was on our CentOS system with the same result. Links OK on SLES9, SLES10 and Ubuntu 11.04. cheers, Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk31xT8ACgkQO2KABBYQAh97UQCeJ5z3YbjYxs4a9gjFh+ZiDH6O TjYAnivq6MY0HTuP0xjc5wx6Vfef+HZc =52rR -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 12/06/11 11:55, Samuel Thibault wrote: > Could you look for this in your /usr/include? $ grep -R __res_query /usr/include/ /usr/include/resolv.h:#define res_query __res_query /usr/include/resolv.h:#define res_querydomain __res_querydomain $ grep -wR res_query /usr/include/ /usr/include/resolv.h:#define res_query __res_query /usr/include/resolv.h:int res_query (const char *, int, int, u_char *, int) __THROW; The symbol itself is only in the .so files, not in any of the object modules, so it looks like it's something being pulled in as a link-time dependency by libtool/ld. $ grep -R res_query . Binary file ./src/.libs/libhwloc.so.0.0.0 matches Binary file ./src/.libs/libhwloc.so matches Binary file ./src/.libs/libhwloc.so.0 matches > I fail to see how that symbol can ever get into > libhwloc.so, as we don't do any network thing at all... I *suspect* it's being pulled in by libpci - here: $ nm /usr/lib/libpci.a | grep res_query U __res_query $ rpm -qf /usr/lib/libpci.a pciutils-devel-3.1.7-3.el5 Oddly that's listed as being in the library on Ubuntu 11.04 too, but it's not ending up in the libhwloc.so on that platform. cheers! Chris - -- Christopher Samuel - Senior Systems Administrator VLSCI - Victorian Life Sciences Computation Initiative Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545 http://www.vlsci.unimelb.edu.au/ -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk30UmQACgkQO2KABBYQAh9Y7QCfRjySIuh4eoN7BEGqJ4BXWLgB KsUAoJaYlF8xKgFrg2NM/a8QIhjdgK9/ =/diu -END PGP SIGNATURE-
Re: [hwloc-devel] hwloc trunk nightly 1.3a1r3511 fails to build on CentOS 5.6 & RHEL 5.6
Christopher Samuel, le Sun 12 Jun 2011 03:43:08 +0200, a écrit : > CCLD lstopo > /tmp/hwloc-1.3a1r3511/src/.libs/libhwloc.so: undefined reference to > `__res_query' Could you look for this in your /usr/include? I fail to see how that symbol can ever get into libhwloc.so, as we don't do any network thing at all... Samuel
