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Old   May 28, 2017, 13:16
Default AD build problem SU2-5.0.0
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Hello,

I'm trying to compile su2 with AD support. When I use this command:
"export CXXFLAGS="-O3 -Wall" && ./preconfigure.py --enable-autodiff --enable-mpi --prefix=$SU2_INSTALLPATH"

I get the following message:

Checking the status of submodules
================================================== ===================
Found an old or unspecified version of CoDiPack in externals/codi.
Use -u to reset module.

Could you please help me resolve the problem?

Thanks
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Old   May 29, 2017, 16:00
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Quote:
Originally Posted by Ryan. View Post
Hello,

I'm trying to compile su2 with AD support. When I use this command:
"export CXXFLAGS="-O3 -Wall" && ./preconfigure.py --enable-autodiff --enable-mpi --prefix=$SU2_INSTALLPATH"

I get the following message:

Checking the status of submodules
================================================== ===================
Found an old or unspecified version of CoDiPack in externals/codi.
Use -u to reset module.

Could you please help me resolve the problem?

Thanks
Hi,

Try removing codi directory inside externals and run preconfigure again. It must download it for you and solve the isuue.
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Old   May 29, 2017, 16:55
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Quote:
Originally Posted by Eman. View Post
Hi,

Try removing codi directory inside externals and run preconfigure again. It must download it for you and solve the isuue.
Problem solved! Thanks.
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Old   October 13, 2017, 10:11
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I encounter the same problem. After remmoving the codi directory and running preconfigure again, I get the following message:


Checking the status of submodules
================================================== ===================

Initializing CoDiPack '2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'
================================================== ===================
Downloading module from https://github.com/scicompkl/CoDiPack
Extracting archive ...
Extraction of module CoDiPack failed. See preconf.err for more information.


So I open the "preconf.err", it shows:

--2017-10-13 22:00:57-- https://github.com/scicompkl/CoDiPac...9244484f13.zip
正在解析主机 github.com (github.com)... 192.30.255.113, 192.30.255.112
正在连接 github.com (github.com)|192.30.255.113|:443... 已连接。
已发出 HTTP 请求,正在等待回应... 302 Found
位置:https://codeload.github.com/SciCompK...6dc69244484f13 [跟随至新的 URL]
--2017-10-13 22:01:01-- https://codeload.github.com/SciCompK...6dc69244484f13
正在解析主机 codeload.github.com (codeload.github.com)... 192.30.255.121, 192.30.255.120
正在连接 codeload.github.com (codeload.github.com)|192.30.255.121|:443... 已连接。
已发出 HTTP 请求,正在等待回应... 200 OK
长度: 未指定 [application/zip] ///length: not specified
正在保存至: “2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip”

0K .......... .......... .......... .......... .......... 75.6K
50K .......... .......... .......... .......... .......... 144K
100K .......... .......... .......... .......... .......... 8.03M
150K .......... .......... .......... .......... .......... 140K
200K .......... .......... .......... .......... ...... 141K=1.7s

缺少“Last-modified”文件头 -- 关闭时间戳标记。 //// translate in English: lack the file header" Last-modified "
2017-10-13 22:01:04 (145 KB/s) - “2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip” 已保存 [252908]

/bin/sh: 1: unzip: not found


I have translate some main sentences. I don't know how to solve this problem, could you please give me some advice?
Thanks.

Last edited by Kaizhi Ding; October 13, 2017 at 10:29. Reason: translate to some words to English
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Old   October 13, 2017, 16:08
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Hi Kaizhi,

it looks like unzip is not installed on your machine. Try to install it with the package manager of your distribution.

Otherwise, if you want to use your preferred unpacking tool try the following steps:

- Download the zip at "https://github.com/scicompkl/CoDiPack/archive/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip"
- Extract the archive to externals/codi
- Execute command 'touch externals/codi/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'
- Run preconfigure.py again

Tim
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Old   October 14, 2017, 03:10
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Quote:
Originally Posted by talbring View Post
Hi Kaizhi,

it looks like unzip is not installed on your machine. Try to install it with the package manager of your distribution.

Otherwise, if you want to use your preferred unpacking tool try the following steps:

- Download the zip at "https://github.com/scicompkl/CoDiPack/archive/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip"
- Extract the archive to externals/codi
- Execute command 'touch externals/codi/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'
- Run preconfigure.py again

Tim
I have solved my problem as you said, thanks for your help!
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Old   November 30, 2017, 00:16
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Quote:
Originally Posted by Eman. View Post
Hi,

Try removing codi directory inside externals and run preconfigure again. It must download it for you and solve the isuue.
Hi, I have a similar problem. I tried removing the codi directory but on running preconfigure again, the script crashes out on downloading a new codi:

Code:
Initializing CoDiPack '2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'
=====================================================================
Downloading module from https://github.com/scicompkl/CoDiPack
Extracting archive ...
Extraction of module CoDiPack failed. See preconf.err for more information.
Inside the file, I see:

Code:
--2017-11-30 14:13:17--  https://github.com/scicompkl/CoDiPack/archive/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip
Resolving github.com... 192.30.255.113, 192.30.255.112
Connecting to github.com|192.30.255.113|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://codeload.github.com/SciCompKL/CoDiPack/zip/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13 [following]
--2017-11-30 14:13:18--  https://codeload.github.com/SciCompKL/CoDiPack/zip/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13
Resolving codeload.github.com... 192.30.255.121, 192.30.255.120
Connecting to codeload.github.com|192.30.255.121|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 252908 (247K) [application/zip]
Last-modified header missing -- time-stamps turned off.
--2017-11-30 14:13:19--  https://codeload.github.com/SciCompKL/CoDiPack/zip/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13
Reusing existing connection to codeload.github.com:443.
HTTP request sent, awaiting response... 200 OK
Length: 252908 (247K) [application/zip]
Saving to: `2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'

     0K .......... .......... .......... .......... .......... 20%  131K 2s
    50K .......... .......... .......... .......... .......... 40%  257K 1s
   100K .......... .......... .......... .......... .......... 60%  256K 0s
   150K .......... .......... .......... .......... .......... 80%  262K 0s
   200K .......... .......... .......... .......... ......    100% 7.85M=1.0s

2017-11-30 14:13:20 (255 KB/s) - `2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13' saved [252908/252908]

unzip:  cannot find or open 2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip, 2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip.zip or 2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip.ZIP.
Is it downloading to the wrong location?
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Old   November 30, 2017, 04:03
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Hi Tim,

just follow the steps I posted also above:


Quote:
Originally Posted by talbring View Post
- Download the zip at "https://github.com/scicompkl/CoDiPack/archive/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13.zip"
- Extract the archive to externals/codi
- Execute command 'touch externals/codi/2ec7cccf3ccd4b052f9d4ef95d6dc69244484f13'
- Run preconfigure.py again
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Old   December 1, 2017, 02:28
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Hi, thanks for the post, it's now producing a similar problem with AdjointMPI...

Code:
Checking the status of submodules
=====================================================================
Found correct version of CoDiPack in externals/codi.
Found an old or unspecified version of AdjointMPI in externals/adjointmpi.
Use -u to reset module.
Are there similar steps I can take here?
Many thanks.
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Old   December 1, 2017, 02:47
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I had a dig around preconfigure.py and I did the same steps as above but grabbing the file from `https://github.com/michel2323/AdjointMPI` and touch on `31b2267c3a55a391a37d830369f2e0dba09008d1`.

I'm wondering if something strange is happening, because now it seems to be having trouble finding configure?

Code:
Checking the status of submodules
=====================================================================
Found correct version of CoDiPack in externals/codi.
Found correct version of AdjointMPI in externals/adjointmpi.

Configuring and building AdjointMPI in externals/adjointmpi
=====================================================================
Command: ./configure --prefix=/home/FIa/FIa164/programs/su2/SU2-5.0.0_src/externals/adjointmpi --with-mpicc=/home/FIa/FIa164/programs/openmpi/openmpi-3.0.0/bin/mpicc && make clean && make

There was an error while running command './configure --prefix=/home/FIa/FIa164/programs/su2/SU2-5.0.0_src/externals/adjointmpi --with-mpicc=/home/FIa/FIa164/programs/openmpi/openmpi-3.0.0/bin/mpicc && make clean && make'.
=== Error Log ===
/bin/sh: ./configure: No such file or directory
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Old   December 1, 2017, 16:52
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Can you check whether the file externals/adjointmpi/configure actually exists ? Maybe the archive was not properly extracted ..
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Old   December 2, 2017, 01:53
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Quote:
Originally Posted by talbring View Post
Can you check whether the file externals/adjointmpi/configure actually exists ? Maybe the archive was not properly extracted ..
There isn't a 'configure' in the directory, but there is a 'configure.ac'. There isn't a configure in the original github link either.
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Old   December 2, 2017, 14:37
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Ok you downloaded the wrong version (i.e. commit). Use this link to download the correct one:

https://github.com/michel2323/Adjoin...dba09008d1.zip
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Old   December 4, 2017, 02:00
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Quote:
Originally Posted by talbring View Post
Ok you downloaded the wrong version (i.e. commit). Use this link to download the correct one:

https://github.com/michel2323/Adjoin...dba09008d1.zip
Hi, thanks for the heads up - I didn't notice this before! This version did the trick.

While building, I'm coming across a different problem (I'm not sure if I should put this in a new issue?) - do you have any experience installing SU2 with OpenBLAS as the lapack library? After setting the flag --with-LAPACK-include=/home/FIa/FIa164/programs/openblas/OpenBLAS-0.2.20/include I notice that SU2 search in the specified PREFIX/include for liblapacke.a (is this some kind of c lapack library?). The problem is that there is no file named this in the OpenBLAS include folder - should I be renaming/symbolic linking to another file in the include directory?

These are the files I have:
Code:
FIa164@afispb07:~/programs/openblas/OpenBLAS-0.2.20/include$ ls
cblas.h  f77blas.h  lapacke_config.h  lapacke.h  lapacke_mangling.h  lapacke_utils.h  openblas_config.h
Thanks for the install support so far. Kind regards, Tim
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