p4est has to be configured with enabled zlib support

[Lev Karatun]

Hi everyone,

I was updating dealII to the latest version and received the error when trying to configure it: 

"  Insufficient p4est installation found!

  p4est has to be configured with enabled zlib support."

I used the p4est-setup.sh script to install it originally (and haven't modified it ever since), could you please let me know how I can modify the script to include zlib support? 

Thanks in advance!

[Bruno Turcksin]

Lev,

you need to make sure that zlib is installed on your machine and then reinstall p4est. zlib should be picked up automatically.

Best,

Bruno

[Lev Karatun]

Hi Bruno,

I reinstalled p4est, but zlib didn't get picked up unfortunately. I made sure it is installed on the machine:

"Installed Packages

Name        : zlib

Arch        : x86_64

Version     : 1.2.3

Release     : 29.el6

Size        : 149 k

Repo        : installed

From repo   : anaconda-CentOS-201410241409.x86_64

Summary     : The zlib compression and decompression library

URL         : http://www.gzip.org/zlib/

License     : zlib and Boost

Description : Zlib is a general-purpose, patent-free, lossless data compression

            : library which is used by many different programs."

Best regards,

Lev Karatun.

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[Timo Heister]

You need the "dev" package too. On my machine it is called zlib1g-dev

On Wed, Apr 26, 2017 at 10:03 AM, Lev Karatun <lev.k...@gmail.com> wrote:
> Hi Bruno,
>
> I reinstalled p4est, but zlib didn't get picked up unfortunately. I made
> sure it is installed on the machine:
> "Installed Packages
> Name : zlib
> Arch : x86_64
> Version : 1.2.3
> Release : 29.el6
> Size : 149 k
> Repo : installed
> From repo : anaconda-CentOS-201410241409.x86_64
> Summary : The zlib compression and decompression library

> URL : https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gzip.org_zlib_&d=DwIBaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=4k7iKXbjGC8LfYxVJJXiaYVu6FRWmEjX38S7JmlS9Vw&m=9tL9gz_PNnuTA1j6uBJk0JEUfIFR-s2tI_KohRB4U3w&s=uLjZ-nmptzLNBPhgUYKYtMzr6CGUXlu2pzVSqPfC5pA&e=

> License : zlib and Boost
> Description : Zlib is a general-purpose, patent-free, lossless data
> compression
> : library which is used by many different programs."
>
> Best regards,
> Lev Karatun.
>
> 2017-04-26 8:35 GMT-04:00 Bruno Turcksin <bruno.t...@gmail.com>:
>>
>> Lev,
>>
>> you need to make sure that zlib is installed on your machine and then
>> reinstall p4est. zlib should be picked up automatically.
>>
>> Best,
>>
>> Bruno
>>
>> On Tuesday, April 25, 2017 at 7:06:21 PM UTC-4, Lev Karatun wrote:
>>>
>>> Hi everyone,
>>>
>>> I was updating dealII to the latest version and received the error when
>>> trying to configure it:
>>> " Insufficient p4est installation found!
>>> p4est has to be configured with enabled zlib support."
>>>
>>> I used the p4est-setup.sh script to install it originally (and haven't
>>> modified it ever since), could you please let me know how I can modify the
>>> script to include zlib support?
>>>
>>> Thanks in advance!
>>
>> --

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Timo Heister
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[Lev Karatun]

Hi Timo,

it's installed too =(

"Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version

Nothing to do"

Best regards,

Lev Karatun.

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[Bruno Turcksin]

Lev,

2017-04-26 10:16 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> it's installed too =(
>
> "Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version
> Nothing to do"

Maybe it's not in your LD_LIBRARY_PATH? How did you install it?

Best

Bruno

[Lev Karatun]

Hi Bruno,

I don't remember installing zlib, maybe it was installed with the OS? Or maybe it was part of some other packages I installed in the past? I'm not sure. Again, I installed p4est on this machine 2 years ago and haven't done anything to it, that's why it seems strange it's not accepted by dealII anymore. 

Anyway, zlib was indeed not in LD_LIBRARY_PATH:

>> rpm -ql zlib-devel.x86_64

/usr/include/zconf.h

/usr/include/zlib.h

/usr/lib64/libz.so

/usr/lib64/pkgconfig/zlib.pc

/usr/share/doc/zlib-devel-1.2.3

/usr/share/doc/zlib-devel-1.2.3/README

/usr/share/doc/zlib-devel-1.2.3/algorithm.txt

/usr/share/doc/zlib-devel-1.2.3/example.c

/usr/share/doc/zlib-devel-1.2.3/minigzip.c

/usr/share/man/man3/zlib.3.gz

I added it (is it correct now?):

>> echo $LD_LIBRARY_PATH

/usr/lib64/openmpi/lib:/opt/rh/devtoolset-2/root/usr/lib64:/opt/rh/devtoolset-2/root/usr/lib:/usr/share/doc/:/usr/include:/usr/lib64

Reinstalled p4est, but still getting the same error.

Best regards,

Lev Karatun.

Bruno

[Bruno Turcksin]

Very strange. Can you go in the build directory of p4est (DEBUG or
FAST it doesn't matter) and run the tests (make tests). Do all the
tests pass?

Bruno

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[Lev Karatun]

Doesn't work =(

"[lev@titan FAST]$ pwd

/home/lev/distrib/p4est-build/FAST

[lev@titan FAST]$ l

total 1M

-rw-rw-r--  1 lev lev 1M Apr 26 11:35 config.log

-rw-rw-r--  1 lev lev 1M Apr 26 11:35 config.output

-rw-rw-r--  1 lev lev 1M Apr 26 11:34 _configs.sed

-rwxrwxr-x  1 lev lev 1M Apr 26 11:34 config.status*

drwxrwxr-x 11 lev lev 1M Apr 26 11:34 example/

-rwxrwxr-x  1 lev lev 1M Apr 26 11:35 libtool*

-rw-rw-r--  1 lev lev 1M Apr 26 11:34 Makefile

-rw-rw-r--  1 lev lev 1M Apr 26 11:35 Makefile.p4est.mk

-rw-rw-r--  1 lev lev 1M Apr 26 11:34 Makefile.p4est.pre

-rw-rw-r--  1 lev lev 1M Apr 26 11:35 make.output

drwxrwxr-x  9 lev lev 1M Apr 26 11:35 sc/

drwxrwxr-x  4 lev lev 1M Apr 26 11:35 src/

drwxrwxr-x  3 lev lev 1M Apr 26 11:35 test/

[lev@titan FAST]$ make tests

make: *** No rule to make target `tests'.  Stop."

Best regards,

Lev Karatun.

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[Bruno Turcksin]

2017-04-26 17:10 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> [lev@titan FAST]$ make tests
> make: *** No rule to make target `tests'. Stop."

Sorry it was `make check`

Bruno

[Lev Karatun]

Hi Bruno,

all tests passed. 

Best regards,

Lev Karatun.

Bruno

[Bruno Turcksin]

2017-04-26 18:10 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> all tests passed.
OK Then can you try to configure deal in a new empty directory.

Best

Bruno

[Lev Karatun]

Hi Bruno,

that's what I was doing...

Best regards,

Lev Karatun.

Bruno

[Bruno Turcksin]

2017-04-26 23:10 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> that's what I was doing...

Maybe try candi or spack

Best,

Bruno

[Lev Karatun]

Hi Bruno,

what do you mean by that?..

Best regards,

Lev Karatun.

[Bruno Turcksin]

2017-04-27 14:53 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> what do you mean by that?..

Don't try to install deal.II yourself. candi
(https://github.com/dealii/candi) or spack
(https://github.com/dealii/dealii/wiki/deal.II-in-Spack) can take care
of all the dependencies for you. They are both regularly tested on
multiple platforms.

Best,

Bruno

[Lev Karatun]

Hi Bruno,

Thank you, installing with candi worked (in release mode). Does it support installing in Debug mode (that's was I was trying to do in the first place)? I haven't found an option in the config file..

Best regards,

Lev Karatun.

[Bruno Turcksin]

Lev,

2017-04-28 8:16 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> Thank you, installing with candi worked (in release mode). Does it support
> installing in Debug mode (that's was I was trying to do in the first place)?
> I haven't found an option in the config file..

candi should have installed both the debug and the release version of
the library. Are you sure it didn't work?

Best,

Bruno

[Lev Karatun]

Hi Bruno,

debug version actually was installed too, I just didn't realize. Thank you for your help!

Best regards,

Lev Karatun.

[Lev Karatun]

Hi Bruno,

I was trying to update dealII on a cluster with Trilinos that I didn't even install myself, but loaded using a module manager. I got the exact same error message as before. Is having Trilinos configured with zlib support something that was introduced recently? If not, can it be that dealII is not detecting the installation properly?

Best regards,

Lev Karatun.

[Bruno Turcksin]

Lev

2017-05-04 15:45 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> I was trying to update dealII on a cluster with Trilinos that I didn't even
> install myself, but loaded using a module manager. I got the exact same
> error message as before. Is having Trilinos configured with zlib support
> something that was introduced recently? If not, can it be that dealII is not
> detecting the installation properly?

The problem is not Trilinos, the problem is p4est. If p4est doesn't
find zlib, everything will compile but some needed capabilities of
p4est will be missing. This creates hard to debug bugs when you run
deal. So now we make sure that zlib is installed. So make sure that
both p4est and deal found zlib.

Best,

Bruno

[Lev Karatun]

Hi Bruno,

is this a recently introduced requirement?

Best regards,

Lev Karatun.

[Bruno Turcksin]

Lev,

2017-05-05 1:13 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> is this a recently introduced requirement?

Yes, see the discussion here https://github.com/dealii/dealii/issues/4151

Best,

Bruno

[Lev Karatun]

Hi Bruno,

I see it's mentioned that running make check for p4est should catch the lack of zlib (if I understood it correctly), but in my case all checks ran successfully, which suggests this is not quite the case. 

Also, Timo suggested printing out a warning after installing p4est if zlib was not found, would that be an easy thing to add? I would then be able to check if p4est was indeed installed without zlib. 

Best regards,

Lev Karatun.

[Bruno Turcksin]

Lev,

2017-05-06 23:45 GMT-04:00 Lev Karatun <lev.k...@gmail.com>:
> Also, Timo suggested printing out a warning after installing p4est if zlib
> was not found, would that be an easy thing to add? I would then be able to
> check if p4est was indeed installed without zlib.

I don't know, I am bad with cmake. You can use ldd
(https://en.wikipedia.org/wiki/Ldd_(Unix)) on the p4est library and
see if p4est was built with zlib.

Best,

Bruno