[mpich-discuss] mpich2-1.2.1p1 - cannot create regular file`/index.htm': Permission denied
Scott Atchley
atchley at myri.com
Fri Mar 19 12:38:34 CDT 2010
Hi all,
I ran into the same problem today with 1.2.1p1 on Centos5.4. I had to manually edit src/pm/hydra/Makefile.in and prepend $(top_srcdir) before several mpl items. See the attached patch. After patching, configure and make were happy.
Scott
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On Mar 11, 2010, at 5:01 PM, Pavan Balaji wrote:
>
> No, the point is the user should not need to use autotools at all if
> building from the released tarball.
>
> The problem that was happening was that MPL has some time stamp for
> aclocal.m4 that it creates, and then Hydra goes and overwrites it,
> creating a dependency mess within the Makefile.
>
> -- Pavan
>
> On 03/11/2010 03:53 PM, Anthony Chan wrote:
>> Pavan,
>>
>> This guy's system is pretty old, he does not seem to have the autotools
>> needed to rebuild the configure and Makefile.in involved.
>>
>> A.Chan
>>
>> ----- "Pavan Balaji" <balaji at mcs.anl.gov> wrote:
>>
>>> Ah, I should have seen this earlier. My guess is that you are running
>>> into the autotools ordering issue that we fixed in r6292
>>> (http://trac.mcs.anl.gov/projects/mpich2/changeset/6292).
>>>
>>> Can you try out the latest nightly snapshot to see if the problem
>>> still
>>> exists?
>>>
>>> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/nightly/trunk
>>>
>>> -- Pavan
>>>
>>> On 03/11/2010 03:34 PM, Rajeev Thakur wrote:
>>>> We build MPICH2 quite routinely following the exact steps in the
>>> README
>>>> file, so something strange is happening in your specific case.
>>>>
>>>> Rajeev
>>>>
>>>>
>>> ------------------------------------------------------------------------
>>>> *From:* mpich-discuss-bounces at mcs.anl.gov
>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov] *On Behalf Of
>>> *Preeti
>>>> *Sent:* Thursday, March 11, 2010 1:26 PM
>>>> *To:* mpich-discuss at mcs.anl.gov
>>>> *Subject:* Re: [mpich-discuss] mpich2-1.2.1p1 - cannot create
>>>> regular file`/index.htm': Permission denied
>>>>
>>>> Hi
>>>>
>>>> Thanks for the replies, but I get following errors.
>>>>
>>>> 1. If I do only build in /tmp
>>>> cannot create regular file `/index.htm': Permission denied
>>>>
>>>> 2. if I do everything in /tmp, then the following error.
>>>> " Making all in mpl
>>>> /bin/sh: line 17: cd: mpl: No such file or directory
>>>> make[3]: *** [all-recursive] Error 1"
>>>>
>>>> I have sent both log files earlier.
>>>> Yes, the /home/vss is network file system. I have no root access
>>> to
>>>> the system.
>>>>
>>>> Is there any way out of this?
>>>> Please help.
>>>>
>>>>
>>>> Thanks
>>>> Preeti
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Mar 11, 2010 at 11:18 PM, Rajeev Thakur
>>> <thakur at mcs.anl.gov
>>>> <mailto:thakur at mcs.anl.gov>> wrote:
>>>>
>>>> Just untar and build it again on a local disk. The install
>>> directory
>>>> (--prefix option to configure) can be on NFS.
>>>>
>>>> Rajeev
>>>>
>>>>> -----Original Message-----
>>>>> From: mpich-discuss-bounces at mcs.anl.gov
>>>> <mailto:mpich-discuss-bounces at mcs.anl.gov>
>>>>> [mailto:mpich-discuss-bounces at mcs.anl.gov
>>>> <mailto:mpich-discuss-bounces at mcs.anl.gov>] On Behalf Of
>>>>> chan at mcs.anl.gov <mailto:chan at mcs.anl.gov>
>>>>> Sent: Thursday, March 11, 2010 11:48 AM
>>>>> To: mpich-discuss at mcs.anl.gov
>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>> Subject: Re: [mpich-discuss] mpich2-1.2.1p1 - cannot
>>> create
>>>>> regular file `/index.htm': Permission denied
>>>>>
>>>>>
>>>>> Is your /home/vss a local filesystem or some type
>>>>> network file system ? If /home/vss is a network
>>>>> filesystem, the problem could be incorrect clock
>>>>> on the filesystem. If so, could you copy
>>>>> everything to a local filesystem like /tmp(assuming
>>>>> it is big enough) and try again ?
>>>>>
>>>>> ----- "Preeti" <preeti at csa.iisc.ernet.in
>>>> <mailto:preeti at csa.iisc.ernet.in>> wrote:
>>>>>
>>>>>> Hello
>>>>>>
>>>>>> I have rebuilt everything without setting the flags
>>> also
>>>>>>
>>>>>> /home/vss/preeti/bin/mpich2-1.2.1p1/configure
>>>>>> --prefix=/home/vss/preeti/bin/2-1.2.1build --enable-f90
>>> 2>&1
>>>> | tee
>>>>>> c.log
>>>>>>
>>>>>> make 2>&1 | tee m.log
>>>>>> make install 2>&1 | tee mi.log
>>>>>>
>>>>>>
>>>>>> and this time I get the following error
>>>>>>
>>>>>> /usr/bin/install -c -m 644 index.htm /index.htm
>>>>>> /usr/bin/install: cannot create regular file
>>> `/index.htm':
>>>>> Permission
>>>>>> denied
>>>>>> mkdir: cannot create directory `/www1': Permission
>>> denied
>>>>>>
>>>>>>
>>>>>> The log files are attached.
>>>>>> What am I missing?
>>>>>>
>>>>>> Appreciate your help.
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>> Preeti
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Thu, Mar 11, 2010 at 4:37 PM, Preeti
>>>> <preeti at csa.iisc.ernet.in
>>> <mailto:preeti at csa.iisc.ernet.in>>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello
>>>>>>>
>>>>>>> I have rebuilt everything from scratch and did vpath
>>> build.
>>>>>>> I set the following
>>>>>>>
>>>>>>>
>>>>>>> export F90=gfortran
>>>>>>> export F77=gfortran
>>>>>>> export LD_LIBRARY_PATH=/usr/lib64:/lib:/usr/lib
>>>>>>> export LD_RUN_PATH=/usr/lib64:/lib:/usr/lib
>>>>>>>
>>>>>>> /home/vss/preeti/bin/mpich2-1.2.1p1/configure
>>>>>>> --prefix=/home/vss/preeti/bin/2-1.2.1p1 --enable-f90
>>> 2>&1
>>>> | tee
>>>>>> c.log
>>>>>>>
>>>>>>> make 2>&1 | tee m.log
>>>>>>>
>>>>>>>
>>>>>>> Then I get the error
>>>>>>>
>>>>>>> Making all in mpl
>>>>>>> /bin/sh: line 17: cd: mpl: No such file or directory
>>>>>>>
>>>>>>> make[3]: *** [all-recursive] Error 1
>>>>>>>
>>>>>>> The files are attached.
>>>>>>> Please help.
>>>>>>>
>>>>>>>
>>>>>>> Thanks
>>>>>>> Preeti
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Mar 11, 2010 at 1:53 AM, <chan at mcs.anl.gov
>>>> <mailto:chan at mcs.anl.gov>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> I don't think setting F77 and F90 causes the problem
>>> that
>>>>>>>> you are seeing. The directories or subpackges that
>>> have
>>>>>>>> problems use a different build system than the
>>> majority of
>>>>>>>> mpich2 base, so it could be that there is bugs in
>>> the
>>>>> build system
>>>>>>>> in those subpackage.
>>>>>>>>
>>>>>>>> Since you didn't do "make distclean" before you
>>>> reconfigure, so
>>>>>>>> the m.log(.old) do not tell me much. Can you rebuild
>>>> everything
>>>>>>>> from scratch ? i.e. untar the mpich2 tarball in a
>>> different
>>>>>> location.
>>>>>>>> Instead of doing an inpath build (i.e. cd
>>> mpich2-1.2.1p1/ ;
>>>>>>>> ./configure....),
>>>>>>>> could you do a VPATH build as documented in the
>>> README
>>>>> (search for
>>>>>> the
>>>>>>>> word VPATH)? Send us the configure and make outputs
>>> again
>>>>>>>> (be sure to add 2>&1 in creating the output files).
>>>>>>>>
>>>>>>>> A.Chan
>>>>>>>>
>>>>>>>>
>>>>>>>> ----- "Preeti" <preeti at csa.iisc.ernet.in
>>>> <mailto:preeti at csa.iisc.ernet.in>> wrote:
>>>>>>>>
>>>>>>>>> Hello
>>>>>>>>>
>>>>>>>>> Thank you for the quick response.
>>>>>>>>>
>>>>>>>>> I forgot to mention that I had set two flags
>>> earlier.
>>>>>>>>> export F90=gfortran
>>>>>>>>> export F77=gfortran
>>>>>>>>>
>>>>>>>>> The earlier problem is gone when I compiled without
>>> setting
>>>>>> these. I
>>>>>>>>> am
>>>>>>>>> attaching all log files, the earlier ones and the
>>> new ones.
>>>>>>>>>
>>>>>>>>> Now I am facing another error which is from "make
>>>> install 2>& |
>>>>>> tee
>>>>>>>>> mi.log"
>>>>>>>>>
>>>>>>>>> /usr/bin/install: cannot create regular file
>>> `/index.htm':
>>>>>> Permission
>>>>>>>>> denied
>>>>>>>>>
>>>>>>>>> Probably some variable is not set. I tried setting
>>>> docdir too.
>>>>>>>>> mi.log is also attached.
>>>>>>>>>
>>>>>>>>> Please help.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>> Preeti
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Mar 10, 2010 at 9:33 PM, <chan at mcs.anl.gov
>>>> <mailto:chan at mcs.anl.gov>> wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> It is unclear what went wrong based on what
>>> you've
>>>>> provided so
>>>>>> far.
>>>>>>>>>> Can you send us the configure and make outputs
>>> as
>>>> stated in
>>>>>> the
>>>>>>>>>> README (be sure to include the stderr in the
>>> output
>>>> file) ?
>>>>>>>>>>
>>>>>>>>>> ----- "Preeti" <preeti at csa.iisc.ernet.in
>>>> <mailto:preeti at csa.iisc.ernet.in>> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hello
>>>>>>>>>>>
>>>>>>>>>>> I am trying to install mpich2-1.2.1p1 on a
>>> 64-bit Linux
>>>>>> system.
>>>>>>>>>>>
>>>>>>>>>>> Configuration was successful.
>>>>>>>>>>> ./configure --prefix=$HOME/local/mpich2-1.2.1
>>>>> --enable-f90 |
>>>>>> tee
>>>>>>>>>>> c.log
>>>>>>>>>>
>>>>>>>>>> BTW, you didn't include stderr in c.log. Depends
>>> on
>>>>> the shell
>>>>>> you
>>>>>>>>>> use, you need to either add "&" or "2>&1". See
>>>> README for
>>>>>>>>> details..
>>>>>>>>>>
>>>>>>>>>> A.Chan
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> mpich-discuss mailing list
>>>>>>>>>> mpich-discuss at mcs.anl.gov
>>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>>>>>>>
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> This message has been scanned for viruses and
>>>>>>>>>> dangerous content by MailScanner, and is
>>>>>>>>>> believed to be clean.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> mpich-discuss mailing list
>>>>>>>>> mpich-discuss at mcs.anl.gov
>>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>>>>>>
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>> _______________________________________________
>>>>>>>> mpich-discuss mailing list
>>>>>>>> mpich-discuss at mcs.anl.gov
>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>>>>>
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>>>>
>>>>>>>> --
>>>>>>>> This message has been scanned for viruses and
>>>>>>>> dangerous content by MailScanner, and is
>>>>>>>> believed to be clean.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> mpich-discuss mailing list
>>>>>> mpich-discuss at mcs.anl.gov
>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>>>
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>> _______________________________________________
>>>>> mpich-discuss mailing list
>>>>> mpich-discuss at mcs.anl.gov
>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>>
>>>>
>>>> _______________________________________________
>>>> mpich-discuss mailing list
>>>> mpich-discuss at mcs.anl.gov
>>> <mailto:mpich-discuss at mcs.anl.gov>
>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>>>
>>>> --
>>>> This message has been scanned for viruses and
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>>>>
>>>>
>>>>
>>> ------------------------------------------------------------------------
>>>> _______________________________________________
>>>> mpich-discuss mailing list
>>>> mpich-discuss at mcs.anl.gov
>>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>>> --
>>> Pavan Balaji
>>> http://www.mcs.anl.gov/~balaji
>>> _______________________________________________
>>> mpich-discuss mailing list
>>> mpich-discuss at mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>> _______________________________________________
>> mpich-discuss mailing list
>> mpich-discuss at mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
>
> --
> Pavan Balaji
> http://www.mcs.anl.gov/~balaji
> _______________________________________________
> mpich-discuss mailing list
> mpich-discuss at mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
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