Error during p4est installation

[Lev Karatun]

Hello!

I'm trying to install p4est on a Linux cluster as described here: http://www.dealii.org/developer/external-libs/p4est.html

I'm executing the setup script, but I'm getting the following error:

Build FAST version in /home/r/russ/lkaratun/distrib/aspect/p4est-build/FAST

configure: error: MPI C test failed

Error: Error in configure

I tested MPI by executing "mpirun -np 2 echo a", and got 2 a's as intended. So I'm not quite sure how do I get the script to see MPI.

Could you please help me with it?

Thanks in advance!

Lev.

[Timo Heister]

This is probably because CC is pointing to a non MPI compiler. What
version of p4est are you using? You can dig into the p4est-build
directory and check the config.log file to see what the problem is.

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[Lev Karatun]

Hi Timo, thanks for the reply!

You're right, CC is currently pointing at gcc, not mpicc. Can you please tell me how can I change it? I didn't find any mention of gcc neither in setup script nor in configure script in p4est.

Lev.

[Lei Qiao]

Run " CC=mpicc ./configure --blablabla"

[Lev Karatun]

Thanks Lei, it worked!

Lev.

[Wolfgang Bangerth]

On 05/26/2015 09:49 AM, Lam DANG wrote:
> Hello
>
> I'm trying to install p4est on a Ubuntu by a command line /$ sh
> ./p4est-setup.sh p4est-1.1.tar.gz ./p4est/ from the folder contained
> p4est-1.1.tar.gz and p4est-setup.sh posted in link
> https://www.dealii.org/developer/external-libs/p4est.html
>
> An error is below:
> /./p4est-setup.sh: 31: ./p4est-setup.sh: Syntax error: "(" unexpected/

The problem is that you execute the script via 'sh':

$ sh ./p4est-setup.sh p4est-1.1.tar.gz

You need to execute it with 'bash' instead, i.e., you need to say

$ bash ./p4est-setup.sh p4est-1.1.tar.gz

or just say this:

$ ./p4est-setup.sh p4est-1.1.tar.gz


Best
W.

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Wolfgang Bangerth email: bang...@math.tamu.edu
www: http://www.math.tamu.edu/~bangerth/

[D. Sarah Stamps]

I am having the same issue as Lev. What is the end of the command:

"CC=mpicc ./configure --??" 

Thanks,

DSS

[Bruno Turcksin]

On Tuesday, July 28, 2015 at 2:34:20 PM UTC-5, D. Sarah Stamps wrote:

I am having the same issue as Lev. What is the end of the command:

"CC=mpicc ./configure --??" 

You can just do:

export CC=mpicc

and then run the setup script normally.

Best,

Bruno

[D. Sarah Stamps]

Hmm, still the same issue. Attached is my config.log file. Can you see any issues?

Thank you,

DSS 

[Bruno Turcksin]

On 07/28/2015 03:06 PM, D. Sarah Stamps wrote:
> Hmm, still the same issue. Attached is my config.log file. Can you see
> any issues?

For some reason CC still uses gcc instead of mpicc. Are you sure there
was no typo? Do you do export CC=mpicc and then, in the same terminal
run the setup script? What do you get when you type in the terminal:

echo ${SHELL}

Bruno

[D. Sarah Stamps]

I'm running bash. I tried setting CC to mpicc in my .bashrc, but still no luck. i.e. echo $CC gives me: 

/opt/apps/gcc4_7/mvapich2/1.9a2/bin/mpicc

Is there a recommended place to change the install script to force the correct compilers? 

Thank you. 

[Bruno Turcksin]

You could try to delete the p4est-build directory or any other p4est
directory except for the tarball. Maybe some variable where cached.

On 07/28/2015 03:34 PM, D. Sarah Stamps wrote:
> I'm running bash. I tried setting CC to mpicc in my .bashrc, but still
> no luck. i.e. echo $CC gives me:
>
> /opt/apps/gcc4_7/mvapich2/1.9a2/bin/mpicc
>
> Is there a recommended place to change the install script to force the
> correct compilers?

The script does nothing exceptional, you can configure p4est yourself using:

./configure --enable-mpi --enable-shared --disable-vtk-binary
--without-blas --prefix=/home/dstamps/packages/p4est CC=mpicc CFLAGS=-O2

then just type make install

Bruno

[D. Sarah Stamps]

Thank you. p4est configured and compiled. 

I had to also explicitly set CXX=mpicxx. In the end I configured p4est with: 

./configure --enable-mpi --enable-shared --disable-vtk-binary --without-blas --prefix=/home/dstamps/packages/p4est CC=mpicc CFLAGS=-O2  CXX=mpicxx

[fea...@gmail.com]

Dear all,

I also get a bug when I install  p4est
Error: Main header file missing

How can I solve this bugs in the installation of p4est?

Warm regards,
Yaakov

[Wolfgang Bangerth]

On 11/27/2017 08:51 PM, fea...@gmail.com wrote:
>
> I also get a bug when I install p4est

> *Error: Main header file missing
> *

> How can I solve this bugs in the installation of p4est?

That is not enough information for us to tell you what the problem may be. Can
you elaborate?

Best
W.

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------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[FEAPMAN Yaakov]

Dear Prof. Bangerth,

I used follwing command in terminal, and get an error report

bash ./p4est-setup.sh p4est-1.1.tar.gz /home/feapman/Program/p4est-develop
CFLAGS_FAST: -O2
CFLAGS_DEBUG: -O0 -g

This script tries to unpack, configure and build the p4est library.
Build FAST: /home/feapman/Program/p4est-build/FAST
Build DEBUG: /home/feapman/Program/p4est-build/DEBUG
Install FAST: /home/feapman/Program/p4est-develop/FAST
Install DEBUG: /home/feapman/Program/p4est-develop/DEBUG
Checking environment: CFLAGS P4EST_CFLAGS_FAST P4EST_CFLAGS_DEBUG
Unpack directory: /home/feapman/Program/p4est-1.1
Source directory found (remove it to unpack anew)

Error: Main header file missing

Actually,  I really need plug-in p4est as I have to use it for a used defined benchmark in Deal.II. Still Now, I have no idea how to install it.

Warm regards,

Yaakov

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[Daniel Arndt]

Yaakov,

looking at p4est-install.sh, the error tells you that "SRCDIR/src/p4est.h" can't be found.

This might mean that your p4est-1.1.tar.gz is broken or incomplete.

Can you make sure that "src/p4est.sh" indeed exists after unpacking the archive?

If not, try to download p4est-1.1.tar.gz again.

Best,

Daniel

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[fea...@gmail.com]

Hi Daniel,

Now this problem is solved. I would like to ask why I get two orders.

one is defined order p4est
new one is p4est-build

Warm regards,
Yaakov

[Bruno Turcksin]

Yaakov,

2017-12-01 8:26 GMT-05:00 <fea...@gmail.com>:

one is defined order p4est
new one is p4est-build

p4est: directory where you wanted to install p4est

p4est-build: directory where p4est is compiled. This can be removed once p4est is installed.

It is common when you install a library to have three directories: source directory, build directory, and install directory

Best,

Bruno

[fea...@gmail.com]

Hi Bruno & DEAL.ii Team,

many thanks for your suggestion & help!

now I install p4est in a new order which contains three directories: source directory, build directory, and install directory

Warm regards,
Yaakov

[Mark Ma]

Thanks Bruno, it works for my case in a supercomputer.

For some clusters, use module load xxxx before compiling.

To buid the p4est, edit in p4est-setup.sh to add

1. module load xxxx

2. export CC=mpicc, CXX=mpicxx

then use bash ./p4est-setup.sh p4est-x.x.tar.gz install_locations

Mark

在 2015年7月28日星期二 UTC+2下午10:25:41，Bruno Turcksin写道：