Dear researchers,
I am a beginner trying to use CASTEP standalone mode in Ubuntu. When I try to "make" the file, there are lots of notice say "Target xxxxxxx.o does not exit, compilation forced" did anyone encounter this problem?
Is this due to one (or more) part of my system is not correctly prepared? I tried to update my system and tools to newest version, but doesn't work. Do I need a specific old version of each parts such as mpi mkl gfortran or others?
By the way, I can finally get castep.serial or castep.mpi under linux_x86_64_gfortran-serial or mpi, but when I try to run it with "castep.serial" it always say command not found, even I just want to open the build-in help-file. Does it mean a incorrect installation?
Sorry to write such a long question, and thanks for your help in advance.
Compilation messages
"Target xxxxxxx.o does not exist, compilation forced"
The compilation messages can look a bit worrying, but this message is actually completely normal. The message means that the build system looked to see whether you had an up-to-date version of that object already compiled, but it couldn't find any compiled version, so it had to compile it. This will always happen the first time you build CASTEP, since you haven't compiled any of it yet!
Linux doesn't find CASTEP
"when I try to run it with "castep.serial" it always say command not found"
The CASTEP executable will be put (by default) in a subdirectory of the main CASTEP directory. In your case, it should be in the subdirectory:
obj/linux_x86_64_gfortran--serial (for the serial build)
obj/linux_x86_64_gfortran--mpi (for the MPI parallel build)
When you type "castep.serial", Linux doesn't know where that command is, so it looks in the places where programs are usually put (often /bin, /sbin, /usr/bin, /usr/sbin, /usr/local/bin and /usr/local/sbin ; "bin" here is short for "binary"). Since CASTEP is not there, it will tell you that it can't find it. Notice in particular that the directory you're in when you type the command is *not* in Linux's list of usual places to look, which is especially confusing when you first encounter it!
There are several ways to fix this. If you're on a shared machine, the way I'd recommend is to make a subdirectory in your home directory, perhaps called "bin":
mkdir ~/bin
and put CASTEP in there (along with any other programs you compile yourself), e.g.
cp ~/CASTEP-22.1/obj/linux_x86_64_gfortran--serial/castep.serial ~/bin
Now, this still won't mean that Linux will find them, because this is also not a place it will look for programs. The places Linux looks in are stored in a special Linux environment variable called the "path", and the final part of the solution is to add your new directory to this. Exactly how you do this depends on what kind of command-line interpreter (called a "shell") you're using in Linux, but there are only really two main kinds: bash and csh. Type
export PATH=${PATH}:~/bin (if you're using bash)
setenv PATH ${PATH}:~/bin (if you're using csh)
This command tells Linux to look in all the places it's looking in already, and also "~/bin". If you don't know which shell you're using, try typing:
echo $SHELL
and see what it says. If it says something like "/bin/bash" then you're using bash, if it's "/bin/csh" or "/bin/tcsh" then it's csh (or close enough). If it gives something else, just try the line starting "export" and if it gives an error, try the "setenv" one instead!
Now try typing "castep.serial" and you should see this:
Usage:
castep : Run files .cell [and .param]
" [-d|--dryrun] : Perform a dryrun calculation on files .cell
" [-s|--search] : print list of keywords with match in description
" [-v|--version] : print version information
" [-h|--help] : describe specific keyword in .cell or .param
" " all : print list of all keywords
" " basic : print list of basic-level keywords
" " inter : print list of intermediate-level keywords
" " expert : print list of expert-level keywords
" " dummy : print list of dummy keywords
Hopefully, that's all working by this point. The only other thing you need to do is to make sure that your directory is added to the PATH variable every time you log in or open a new terminal -- the way we've done it, it is only added to the current terminal window. If you're using bash, edit the file "~/.bashrc" with a text editor (e.g. gedit), go to the end, and add the line to set the PATH:
export PATH=${PATH}:~/bin
Note that the file is in your home directory ("~/"), and the name starts with a dot ("." a full stop). Save and exit, and it should all be set up for you. If you're using csh, edit the file "~/.cshrc" instead, and add the appropriate line to set the PATH:
setenv PATH ${PATH}:~/bin
Save and exit, and it should all be set up for you.
see this solution
https://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/content/modules/castep/tskcasteprunstandalone.htm
Thank you very much Rene and Adnan, these resources help a lot! Adnan Majeed Rene Dettenborn
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