November 2013 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

I have created the file mpd.hosts in /etc folder in the root , but still it shows the same error ... /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255 On Thu, Nov 7, 2013 at 8:45 AM, Ricardo Román Brenes < roman.ricardo(a)gmail.com> wrote: > You need to create a mpd.hosts in /etc if you want to run mpd as root > On Nov 6, 2013 5:41 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> wrote: > >> Hi, >> >> I am getting the following error while using the command - >> >> [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt >> >> Error - >> >> /usr/bin/mpdroot: open failed for root's mpd conf >> filempiexec_localhost.localdomain (__init__ 1208): forked process failed; >> status=255 >> >> I complied gromacs using - ./configure --enable-shared --enable-mpi. I >> have installed the mpich package , this is what I get when I check for >> mpirun and mpiexec - >> >> [root@localhost /]# which mpirun >> /usr/bin/mpirun >> [root@localhost /]# which mpiexec >> /usr/bin/mpiexec >> >> What could be the problem here ?? >> >> Thanks >> -------- >> Bharat >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Bharat Ph.D. Candidate Biomolecular Engineering Laboratory Pusan National University South Korea Mobile no. - 010-5818-3680

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Re: [mpich-discuss] MPICH error on CentOS
by Ricardo Román Brenes 06 Nov '13

06 Nov '13

You need to create a mpd.hosts in /etc if you want to run mpd as root On Nov 6, 2013 5:41 PM, "bharat gupta" <bharat.85.monu(a)gmail.com> wrote: > Hi, > > I am getting the following error while using the command - > > [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt > > Error - > > /usr/bin/mpdroot: open failed for root's mpd conf > filempiexec_localhost.localdomain (__init__ 1208): forked process failed; > status=255 > > I complied gromacs using - ./configure --enable-shared --enable-mpi. I > have installed the mpich package , this is what I get when I check for > mpirun and mpiexec - > > [root@localhost /]# which mpirun > /usr/bin/mpirun > [root@localhost /]# which mpiexec > /usr/bin/mpiexec > > What could be the problem here ?? > > Thanks > -------- > Bharat > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] MPICH error on CentOS
by bharat gupta 06 Nov '13

06 Nov '13

Hi, I am getting the following error while using the command - [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt Error - /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255 I complied gromacs using - ./configure --enable-shared --enable-mpi. I have installed the mpich package , this is what I get when I check for mpirun and mpiexec - [root@localhost /]# which mpirun /usr/bin/mpirun [root@localhost /]# which mpiexec /usr/bin/mpiexec What could be the problem here ?? Thanks -------- Bharat

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Re: [mpich-discuss] MPICH deploy in an IPv6 environment?
by Ken Raffenetti 06 Nov '13

06 Nov '13

How and when did it fail? Can you provide your configure or make logs for us to look at? Did it successfully install but you are unable to launch jobs? ----- Original Message ----- > From: "沈伟" <shenwei9008(a)sina.com> > To: "discuss-owner" <discuss-owner(a)lists.mpich.org> > Sent: Wednesday, November 6, 2013 10:05:10 AM > Subject: MPICH deploy in an IPv6 environment? > > > I tried to deploy MPICH2 in an IPv6 environment. But failed finally. > I check the source code, and find MPICH2 can support IPv6. Please > how to configure MPICH2 enable it in an IPv6 environment. >

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Antonio J. Peña 06 Nov '13

06 Nov '13

Thanks for the reminder Pavan. I know that, but sometimes I forget when giving assistance, as we use them extensively. Mogesh, please forget about libtool, and check Junchao's suggestion based on your log files. Sorry for the mess. Toni On Wednesday, November 06, 2013 03:00:46 AM Pavan Balaji wrote: > Hi Toni, > > Users should never have to use autotools. Those are only for us (i.e., > developers). The release tarballs should already have the generated > configure and friends. > > —- Pavan > > On Nov 5, 2013, at 12:44 PM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Hi Mogesh, > > > > We'll need some more information to be able to help you. What's your OS? > > Libtool version? Please also attach config.log and your complete c.txt. > > Your generated libtool script is going to be useful as well. I wonder why > > your libtool looks for that file at all.> > > Antonio > > > > On Tuesday, November 05, 2013 02:52:11 PM Mogesh Naidoo wrote: > > Hi, > > > > I'm having trouble compiling MPICH-3.0.4. > > I'm using GNU 4.7.2 compilers. > > My configure = > > ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU > > --with-gnu-ld 2>&1 | tee c.txt Configure is successful with no errors. > > > > The make fails with > > "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" > > This occurs when trying: > > "CCLD libhwloc_embedded.la" > > > > So there's a libxml2.la in /usr/lib64, but there's also one in another > > directory. I add this directory to LD_LIBRARY_PATH and I still get the > > same error. How do I tell make to use the libxml2.la in the other > > directory? > > > > regards, > > Mogesh. > > -- > Pavan Balaji > http://www.mcs.anl.gov/~balaji > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Antonio J. Peña Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory 9700 South Cass Avenue, Bldg. 240, Of. 3148 Argonne, IL 60439-4847 (+1) 630-252-7928 apenya(a)mcs.anl.gov www.mcs.anl.gov/~apenya

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Junchao Zhang 06 Nov '13

06 Nov '13

It seems the compilation was stuck at hwloc. Try export these two env variables and compile again. HWLOC_LIBXML2_CFLAGS = -I<path to your xml2 headers, such as /usr/include/libxml2> HWLOC_LIBXML2_LIBS = -L<path to your xml2 library> -lxml2 If it does not work, could you paste your $LD_LIBRARY_PATH? --Junchao Zhang On Tue, Nov 5, 2013 at 6:52 AM, Mogesh Naidoo <MNaidoo4(a)csir.co.za> wrote: > Hi, > > I'm having trouble compiling MPICH-3.0.4. > I'm using GNU 4.7.2 compilers. > My configure = > ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU > --with-gnu-ld 2>&1 | tee c.txt > Configure is successful with no errors. > > The make fails with > "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" > This occurs when trying: > "CCLD libhwloc_embedded.la" > > So there's a libxml2.la in /usr/lib64, but there's also one in another > directory. > I add this directory to LD_LIBRARY_PATH and I still get the same error. > How do I tell *make* to use the libxml2.la in the other directory? > > regards, > Mogesh. > > > -- > This message is subject to the CSIR's copyright terms and conditions, > e-mail legal notice, and implemented Open Document Format (ODF) standard. > The full disclaimer details can be found at > http://www.csir.co.za/disclaimer.html. > > > This message has been scanned for viruses and dangerous content by > *MailScanner* <http://www.mailscanner.info/>, > and is believed to be clean. > > > Please consider the environment before printing this email. > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Pavan Balaji 06 Nov '13

06 Nov '13

Hi Toni, Users should never have to use autotools. Those are only for us (i.e., developers). The release tarballs should already have the generated configure and friends. —- Pavan On Nov 5, 2013, at 12:44 PM, Antonio J. Peña <apenya(a)mcs.anl.gov> wrote: > > Hi Mogesh, > > We'll need some more information to be able to help you. What's your OS? Libtool version? Please also attach config.log and your complete c.txt. Your generated libtool script is going to be useful as well. I wonder why your libtool looks for that file at all. > > Antonio > > > On Tuesday, November 05, 2013 02:52:11 PM Mogesh Naidoo wrote: > Hi, > > I'm having trouble compiling MPICH-3.0.4. > I'm using GNU 4.7.2 compilers. > My configure = > ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU --with-gnu-ld 2>&1 | tee c.txt > Configure is successful with no errors. > > The make fails with > "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" > This occurs when trying: > "CCLD libhwloc_embedded.la" > > So there's a libxml2.la in /usr/lib64, but there's also one in another directory. > I add this directory to LD_LIBRARY_PATH and I still get the same error. > How do I tell make to use the libxml2.la in the other directory? > > regards, > Mogesh. > > -- > This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. > The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. > > This message has been scanned for viruses and dangerous content by MailScanner, > and is believed to be clean. > > > Please consider the environment before printing this email. > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Mogesh Naidoo 06 Nov '13

06 Nov '13

Hi Antonio, Thanks for having a look. OS: Centos 5.8 (Final) libtool: ltmain.sh (GNU libtool) 1.5.22 (1.1220.2.365 2005/12/18 22:14:06) I've attached a tar of the config.log, c.txt and m.txt. Where can I find the generated libtool script? regards, Mogesh. >>> Antonio J. Peña<apenya(a)mcs.anl.gov> 05/11/2013 20:44 >>> Hi Mogesh, We'll need some more information to be able to help you. What's your OS? Libtool version? Please also attach config.log and your complete c.txt. Your generated libtool script is going to be useful as well. I wonder why your libtool looks for that file at all. Antonio On Tuesday, November 05, 2013 02:52:11 PM Mogesh Naidoo wrote: Hi, I'm having trouble compiling MPICH-3.0.4. I'm using GNU 4.7.2 compilers. My configure = ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU --with-gnu-ld 2>&1 | tee c.txt Configure is successful with no errors. The make fails with "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" This occurs when trying: "CCLD libhwloc_embedded.la" So there's a libxml2.la in /usr/lib64, but there's also one in another directory. I add this directory to LD_LIBRARY_PATH and I still get the same error. How do I tell make to use the libxml2.la in the other directory? regards, Mogesh. -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner ( http://www.mailscanner.info/) , and is believed to be clean. Please consider the environment before printing this email. -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner ( http://www.mailscanner.info/) , and is believed to be clean. Please consider the environment before printing this email. -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Please consider the environment before printing this email.

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Re: [mpich-discuss] Compilation: MPICH3 and libxml2
by Antonio J. Peña 05 Nov '13

05 Nov '13

Hi Mogesh, We'll need some more information to be able to help you. What's your OS? Libtool version? Please also attach config.log and your complete c.txt. Your generated libtool script is going to be useful as well. I wonder why your libtool looks for that file at all. Antonio On Tuesday, November 05, 2013 02:52:11 PM Mogesh Naidoo wrote: Hi, I'm having trouble compiling MPICH-3.0.4. I'm using GNU 4.7.2 compilers. My configure = ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU -- with-gnu-ld 2>&1 | tee c.txt Configure is successful with no errors. The make fails with "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" This occurs when trying: "CCLD libhwloc_embedded.la" So there's a libxml2.la in /usr/lib64, but there's also one in another directory. I add this directory to LD_LIBRARY_PATH and I still get the same error. How do I tell /make/ to use the libxml2.la in the other directory? regards, Mogesh. -- This message is subject to the CSIR's copyright terms and conditions, e- mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html[1]. *MailScanner[2]*, and is believed to be clean. -------- [1] http://www.csir.co.za/disclaimer.html [2] http://www.mailscanner.info/

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Compilation: MPICH3 and libxml2
by Mogesh Naidoo 05 Nov '13

05 Nov '13

Hi, I'm having trouble compiling MPICH-3.0.4. I'm using GNU 4.7.2 compilers. My configure = ./configure --prefix=/export/home/mnaidoo/software/mpich/mpich3_GNU --with-gnu-ld 2>&1 | tee c.txt Configure is successful with no errors. The make fails with "libtool: link: `/usr/lib64/libxml2.la' is not a valid libtool archive" This occurs when trying: "CCLD libhwloc_embedded.la" So there's a libxml2.la in /usr/lib64, but there's also one in another directory. I add this directory to LD_LIBRARY_PATH and I still get the same error. How do I tell make to use the libxml2.la in the other directory? regards, Mogesh. -- This message is subject to the CSIR's copyright terms and conditions, e-mail legal notice, and implemented Open Document Format (ODF) standard. The full disclaimer details can be found at http://www.csir.co.za/disclaimer.html. This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. Please consider the environment before printing this email.

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