error: newly created file is older than distributed files!

[Reimundo Heluani]

Hello, I asked shell access to a larger computer at my institution (192
threads and a couple terabytes of RAM). This is not a computer that I have
root access. I am trying to build sage from git and I hit a configure error on
every package with the message

"newly created file is older than distributed files!"

The snippet that fails is:

# Do 'set' in a subshell so we don't clobber the current shell's
# arguments. Must try -L first in case configure is actually a
# symlink; some systems play weird games with the mod time of symlinks
# (eg FreeBSD returns the mod time of the symlink's containing
# directory).
if (
am_has_slept=no
for am_try in 1 2; do
echo "timestamp, slept: $am_has_slept" > conftest.file
set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null`
if test "$*" = "X"; then
# -L didn't work.
set X `ls -t "$srcdir/configure" conftest.file`
fi
if test "$*" != "X $srcdir/configure conftest.file" \
&& test "$*" != "X conftest.file $srcdir/configure"; then

# If neither matched, then we have a broken ls. This can happen
# if, for instance, CONFIG_SHELL is bash and it inherits a
# broken ls alias from the environment. This has actually
# happened. Such a system could not be considered "sane".
as_fn_error $? "ls -t appears to fail. Make sure there is not a broken
alias in your environment" "$LINENO" 5
fi
if test "$2" = conftest.file || test $am_try -eq 2; then
break
fi
# Just in case.
sleep 1
am_has_slept=yes
done
test "$2" = conftest.file
)
then
# Ok.
:
else
as_fn_error $? "newly created file is older than distributed files!
Check your system clock" "$LINENO" 5
fi

But I am not familiar with the build system. I am attaching one of the config
logs that fails and the main configure.log. I'll appreciate any help.

Best,

R.

[Dima Pasechnik]

Do you build on a network file system?

Do they have a "scratch" partition you can use, which is on a local disk?

What you see has to do with "skew clocks" on the fileserver vs the CPU you use.

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[Dima Pasechnik]

A standard way to "fix" this for projects like fplll would be to add
AM_MAINTAINER_MODE macro to configure.ac, regenerate ./configure
and then run configure with --disable-maintainer-mode

[Reimundo Heluani]

I found this which is odd at least to me. The date and timezone on the server
is fine:

heluani@tsunami5:~$ date
sex 17 jul 2020 17:31:38 -03
heluani@tsunami5:~$ touch hello.txt
heluani@tsunami5:~$ ls -l hello.txt
-rw-rw-rw- 1 heluani pesq 0 jul 17 14:31 hello.txt
heluani@tsunami5:~$ TZ="utc" ls -l hello.txt
-rw-rw-rw- 1 heluani pesq 0 jul 17 17:31 hello.txt

So "ls" is not showing the modification time in localtime, this behaviour is
different than every other system I own. I would have guessed this has
something to do with this, until you mentioned the skew clocks.

R.

On Jul 17, Dima Pasechnik wrote:
>Do you build on a network file system?
>Do they have a "scratch" partition you can use, which is on a local disk?
>
>What you see has to do with "skew clocks" on the fileserver vs the CPU you use.
>
>
>

>On Fri, 17 Jul 2020, 21:00 'Reimundo Heluani' via sage-devel, <[1]

> email to [2]sage-devel+...@googlegroups.com.
> To view this discussion on the web visit [3]https://groups.google.com/d/
> msgid/sage-devel/20200717200023.GB589209%40vertex.

>
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>to [4]sage-devel+...@googlegroups.com.
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>sage-devel/
>CAAWYfq34CANhyWT%2BRo7CdfLzpOyBVocbxpHpiZN6WUOO%2B_RcMw%40mail.gmail.com.
>
>References:
>
>[1] mailto:sage-...@googlegroups.com
>[2] mailto:sage-devel%2Bunsu...@googlegroups.com
>[3] https://groups.google.com/d/msgid/sage-devel/20200717200023.GB589209%40vertex
>[4] mailto:sage-devel+...@googlegroups.com
>[5] https://groups.google.com/d/msgid/sage-devel/CAAWYfq34CANhyWT%2BRo7CdfLzpOyBVocbxpHpiZN6WUOO%2B_RcMw%40mail.gmail.com?utm_medium=email&utm_source=footer

[Reimundo Heluani]

On Jul 17, Dima Pasechnik wrote:

>Do you build on a network file system?
>Do they have a "scratch" partition you can use, which is on a local disk?
>
>What you see has to do with "skew clocks" on the fileserver vs the CPU you use.
>

Thanks, yes I think my home is mounted from the network. How would a "scratch"
partition work? I thought that once built, moving the installation was
something very hard.

R
>
>
>
>On Fri, 17 Jul 2020, 21:00 'Reimundo Heluani' via sage-devel, <[1]

> email to [2]sage-devel+...@googlegroups.com.
> To view this discussion on the web visit [3]https://groups.google.com/d/
> msgid/sage-devel/20200717200023.GB589209%40vertex.

>
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[Reimundo Heluani]

On Jul 17, Dima Pasechnik wrote:

>A standard way to "fix" this for projects like fplll would be to add
>AM_MAINTAINER_MODE macro to configure.ac, regenerate ./configure
>and then run configure with --disable-maintainer-mode
>

But I'll have to do this for every pkgs that will be installed? that'll take a
while. But if this is really a matter of having /home mounted over nsf, this
should be something that comes up often I suppose.

R

>To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/CAAWYfq1TaAzp15DrUjd7cy%3DB1hk1e04grFVpZFCY6DpRH215Vg%40mail.gmail.com.

[Dima Pasechnik]

On Fri, Jul 17, 2020 at 9:43 PM 'Reimundo Heluani' via sage-devel
<sage-...@googlegroups.com> wrote:
>
> On Jul 17, Dima Pasechnik wrote:
> >A standard way to "fix" this for projects like fplll would be to add
> >AM_MAINTAINER_MODE macro to configure.ac, regenerate ./configure
> >and then run configure with --disable-maintainer-mode
> >
> But I'll have to do this for every pkgs that will be installed? that'll take a
> while. But if this is really a matter of having /home mounted over nsf, this
> should be something that comes up often I suppose.

fplll is one of few libraries that don't have this fix. I've opened
https://github.com/fplll/fplll/issues/439

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/20200717204336.GA594266%40vertex.

[Reimundo Heluani]

On July 17, 2020 5:56:38 PM GMT-03:00, Dima Pasechnik <dim...@gmail.com> wrote:
>On Fri, Jul 17, 2020 at 9:43 PM 'Reimundo Heluani' via sage-devel
><sage-...@googlegroups.com> wrote:
>>
>> On Jul 17, Dima Pasechnik wrote:
>> >A standard way to "fix" this for projects like fplll would be to add
>> >AM_MAINTAINER_MODE macro to configure.ac, regenerate ./configure
>> >and then run configure with --disable-maintainer-mode
>> >
>> But I'll have to do this for every pkgs that will be installed?
>that'll take a
>> while. But if this is really a matter of having /home mounted over
>nsf, this
>> should be something that comes up often I suppose.
>
>fplll is one of few libraries that don't have this fix. I've opened
>https://github.com/fplll/fplll/issues/439
>

I'm a bit lost, this is happening on every pkgs, from giac to gap and so on.

R

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[Matthias Koeppe]

On Friday, July 17, 2020 at 1:25:51 PM UTC-7, Dima Pasechnik wrote:

A standard way to "fix" this for projects like fplll would be to add
AM_MAINTAINER_MODE macro to configure.ac, regenerate ./configure
and then run configure with --disable-maintainer-mode

We could as well delete configure.ac and Makefile.am in spkg-install.

 

[Dima Pasechnik]

oops, sorry, you're hitting a more fundamental problem, your clock is
really, really skew.
I believe the error you get is from a typical autoconf-generated
configure script.

I am actually surprised that Sage's top ./configure script does not
end with this error.
There isn't much we can do here - please ask for help locally at your
HPC center - surely
they have many complaints like this...



On Fri, Jul 17, 2020 at 10:07 PM 'Reimundo Heluani' via sage-devel

> To view this discussion on the web visit https://groups.google.com/d/msgid/sage-devel/FB5FAA54-543D-4E17-B0EB-A5149786ADEA%40potuz.net.