cellulose-builder on Mac OSX

[Malin Wohlert]

Hi,

This seems like a great program! Unfortunately I've had some troubles making it run on my Mac OSX. I have vmd, NAMD and octave 3.2.4 installed but when trying to run the cellulose-builder I get the following error (multiple times):

sed: 1: "auxiliary_script_for_sed": command a expects \ followed by text

and finally:

Program aborted due to error during octave execution. Octave returned non-zero exit status!

Do you have any idea about what could be wrong here and how I can solve this problem?

Best regards

Malin Wohlert

[Thiago Gomes]

Dear Malin Wohlert,

we'd be glad to help get cellulose-builder running on your system.
Please find attached a version of the program prepared based on the errors you reported, which will not get you the final cellulose crystals yet, but will exit producing some diagnostic files. Could you kindly run this version on your Mac OSX and mail me back
the following files:

auxiliary_script_for_sed, sed.err, uc1, uc2, uc3, uc4

Thank you for using cellulose builder.

Thiago C. F. Gomes

2013/2/25 Malin Wohlert <malinw...@gmail.com>

Malin Wohlert

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[bert...@googlemail.com]

Hi Tiago,

I had the same problem of Malin, trying to run the cellulose builder on osx. Did you manage to solve the problem? I've tried the script you attached to the previous post and I can email them to you.

Thanks a lot in advance.

Luca

[Thiago Gomes]

Dear Luca,

we'd be pleased to help solve the problem. Please, send me the files. I will inspect them and let you know whether I can correct the error or need further testing.

Best Regards,

Thiago

2013/9/10 <bert...@googlemail.com>

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[luca bertinetti]

Hi Thiago,

thanks a lot for the quick answer!! here attached the files you were mentioning in your post.

Muito obrigado.

Luca

[Thiago Gomes]

Dear Luca,

We have probably solved the issue. The problem was that Mac OSX uses a different implementation of sed, known as the BSD sed, whereas Linux uses GNU sed. I have adapted the syntax in several command lines so that both implementations of sed are ok with it.

Please find attached the .tar file for the fix. There are two versions in two different directories within the .tar file. Only version2 is designed to actually work. Could you please kindly test version1 and let me know its error messages and let me know if version2 does really work?

I have implemented the fix for allomorph I-beta only, so please leave the file input.inp as it is for testing. If the fix works, I'll implement it for the remainder allomorphs and release an updated version of the program.

Thank you very much for reporting the error and collaborating in the debug process!

Best wishes,

Thiago

2013/9/10 luca bertinetti <bert...@googlemail.com>

[Leo Bian]

Dear Thiago,

I've tested version2 and it's still failed.

I noticed that in the script file "I-beat.sh", the original sed -i is replaced with sed -i''. For Mac OS sed:

1. For the error: sed: 1: "auxiliary_script_for_sed": command a expects \ followed by text : sed -i should be replaced with sed -i '' (notice the space)
   
2. For the error: sed: illegal option -- r: sed -r should be replace with sed -E . BUT then I get another error: invalid command code C, and I don't know how to fix it.

Finally, I can NOT correctly run the script under Mac OS.

Instead, I install gnu-sed by homebrew and temporarily replace the Mac sed: brew install gnu-sed && cd /usr/bin && sudo mv sed sed.bak && sudo ln -s /usr/local/bin/gsed ./ 

Now I can run the version1 correctly, and easily change back to Mac sed by : cd /usr/bin && sudo mv sed gsed && sudo mv sed.bak sed

Thanks very much for your cellulose-builder, its ability of automation have saved much more time and effort. 

在 2013年9月13日星期五UTC+8上午4时03分56秒，Thiago Gomes写道：

[Thiago Gomes]

Dear Leo,

thank you very much for your report, we are glad to receive it!

The version of cellulose-builder intended for Mac Os was actually a closed beta version, created due to an error report from Luca Bertinetti (which kindly helped us by testing the Mac Os version of the script on his own computer, since I didn´t have a Mac around at the time, and still don´t have one - grazie mille Luca!). Of course, we had the intention to release a public version for Mac Os. However, since January 2014 Google has deprecated the creation of new downloads on the Google Code server, where the cellulose-builder project is hosted. This means that, since January 2014, all projects hosted on Google Code no longer have the ability to create new downloads, which was an awfully bad move, in my humble opinion (and in the opinion of many in the open source community who use Google Code for hosting their projects - please see http://google-opensource.blogspot.com.br/2013/05/a-change-to-google-code-download-service.html for more details and if you wish to see how badly this new Google policy has been received by many in the open source community).

Due to this issue reported by Mac OS users regarding problems with different versions of sed (Mac OS sed, GNU sed) and since we can´t get a new Mac Os version online for the general public (we could still use svn on Google code, so that users could still get new versions of the code using svn checkout, but we think that is too technical for non-developers), we have come up with a different (and hopefully better) solution:

we have decided to establish our own server, so that users will have the ability not only to download cellulose-builder, but also to run it remotely in our server and then download the resulting files. Therefore, if a user doesn´t wish to bother with installation of dependencies he or she will be able to run cellulose-builder online. That should also solve the problem of portability of the code from one platform to another. Of course, new versions of the code will still be available for download, as an open source project should be.

We are sorry it took you some trouble to have cellulose-builder running correctly on your computer, but we are glad you could eventually run the Linux version of it by installing GNU sed using homebrew (which is indeed the most straightforward "fix" at the moment). Also, thanks for sharing that on our mailing list!

Finally, we are glad you found cellulose-builder useful and appreciate your feedback! Please, feel free to contact us anytime should you need anything further, we will be happy to help.

Best wishes,

Thiago

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