پاسخ : کمک در مورد نصب نرم افزار gromacs-4.5.5 (حل شد )

[mohsen ramezani]

با سلام خدمت اساتید محترم
دوستان آموزش نصب نرم افزار gromacs-4.5.5 رو بصورت کامل میخوام
ممنون میشم اگه کامل توضیح بدین تا بتونم بدون دردسر نصبش کنم

[Bijan]

با سلام خدمت اساتید محترم
دستان آموزش نصب نرم افزار gromacs-4.5.5 رو بصورت کامل میخوام
ممنون میشم اگه کامل توضیح بدین تا بتونم بدون دردسر نصبش کنم

تو ترمینال دستورات زیر رو تایپ کن:

کد: [انتخاب]

sudo apt-get update
sudo apt-get install gromacs
یا تو مرکز نرم افزار اوبونتو هستش سرچ کن می یاد

[mohsen ramezani]

بعد از sudo apt-get update
وزدن دستور نصب نووشه های زیر میاد

mohsen@mohsen-MS-7529:~$ sudo apt-get install gromacs
Reading package lists... Done
Building dependency tree       
Reading state information... Done
gromacs is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

چطور باید نرم افزار رو اجرا کنم


در ضمن یکی از دوستان دوتا فایل برای نصب این برنامه به من داد
این فایل اول fftw-3.3.2.tar.gz
این فایل دوم gromacs-4.5.5.tar.gz
 که دستور نصبش هم داخلش بود که با اون فایل نصبش کردم این هم متن install

copy fftw-3.3.2.tar.gz and gromacs-4.5.5 files in /root directory
for fftw:
tar xvzf fftw-3.3.2.tar.gz
cd fftw-3.3.2
./configure --enable-float
make
make install

(Add --enable-sse in "configure" command if your computers have i686 or x86-64 processors)
====
for Gromacs:
cd ..
tar xvzf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5
./configure
make
make install
make links

[Bijan]

برنامه رو سیستمت نصب شده  برای اجراش اگه اوبونتو استفاده میکنی در قسمت dash کلیک کن و برنامه رو سرچ کن یا Alt+f2 رو بزن

[mohsen ramezani]

هرچی اسمش رو میزنم ایکنی به این نام نمیاد
اگه میشه دستور ترمنال واسه ران کردنش بزارید

[mohsen ramezani]

کسی نیست راهنماپی کنه
کممممممممممممممممممک

[Masoud92m]

کسی نیست راهنماپی کنه
کممممممممممممممممممک

این رو ببین

کد: [انتخاب]

http://www.cems.uvm.edu/~smanchu/gromacs_installation.html

[mohsen ramezani]

با سلام مجدد برای نصب دوباره اقدام کردم ولی تو یه مرحله ارور میده

FFTW for Linux

    ./configure  --enable-float  --enable-threads
    make
 
su  (Type in your root password and hit the enter button)
    تو این مرحله ارور میده

اینهم error

mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ su
Password:
su: Authentication failure
mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ sudo
usage: sudo [-D level] -h | -K | -k | -V
usage: sudo -v [-AknS] [-D level] [-g groupname|#gid] [-p prompt] [-u user
            name|#uid]
usage: sudo -l[l] [-AknS] [-D level] [-g groupname|#gid] [-p prompt] [-U user
            name] [-u user name|#uid] [-g groupname|#gid] [command]
usage: sudo [-AbEHknPS] [-C fd] [-D level] [-g groupname|#gid] [-p prompt] [-u
            user name|#uid] [-g groupname|#gid] [VAR=value] [-i|-s] [<command>]
usage: sudo -e [-AknS] [-C fd] [-D level] [-g groupname|#gid] [-p prompt] [-u
            user name|#uid] file ...
mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ su: Authentication failure
No command 'su:' found, did you mean:
 Command 'sum' from package 'coreutils' (main)
 Command 'sur' from package 'subtle' (universe)
 Command 'sup' from package 'sup' (universe)
 Command 'sux' from package 'sux' (universe)
 Command 'su' from package 'login' (main)
su:: command not found
mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ Authentication failur
Authentication: command not found
mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ su
Password:
su: Authentication failure
mohsen@mohsen-MS-7529:~/Desktop/fftw-3.0.1$ sudo
usage: sudo [-D level] -h | -K | -k | -V
usage: sudo -v [-AknS] [-D level] [-g groupname|#gid] [-p prompt] [-u user
            name|#uid]
usage: sudo -l[l] [-AknS] [-D level] [-g groupname|#gid] [-p prompt] [-U user
            name] [-u user name|#uid] [-g groupname|#gid] [command]
usage: sudo [-AbEHknPS] [-C fd] [-D level] [-g groupname|#gid] [-p prompt] [-u
            user name|#uid] [-g groupname|#gid] [VAR=value] [-i|-s] [<command>]
usage: sudo -e [-AknS] [-C fd] [-D level] [-g groupname|#gid] [-p prompt] [-u
            user name|#uid] file ...

make  install

Now to do the double precision version, we need to clean up the tree.

    make  distclean
    ./configure  --enable-threads
    make
    make  install

[mohsen ramezani]

با سلام خدمت دوستان
من مراحل نصب رو طبق دستوری که در این لینک بود

http://www.cems.uvm.edu/~smanchu/gromacs_installation.html

تا مرحله 7 نصب پیش رفتم و فکر کنم که نرم افزار نصب شده البته این پیامی که تو ترمینال میاد

GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.
make[3]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'
make[1]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'

واین کارهایی هست که هنوز مونده و برای تکمیل باید انجام بشه لطفا راهنمایی کنید برای تکمیل نصب باید چکار کنم؟

    Finally to creat the links to the Gromacs programs in /usr/local/bin, you need to type in the next command. Doing this will make your life much easier since when ever you need to run Gromacs, you will just have to type either "grompp" or "grompp-d" instead of going and finding the right executable file in the folder where we installed it and copy it each and every time to different folder where we want do the simulations. Even better, by doing this you can simply type in "gro" or "gr" and press the Tab and you get link/shortcut to your gromacs exectable file which is either "grompp" or "grompp-d" depending on what precision you have compiled your package. "grompp" is the executable file obtained with single precision, where as "grompp_d" is the executable file obtained with double precision compliation.
    make  links
    Even after typing this command, when you press "grom" with out quotes at your command prompt and pressing tab, if you don't get name of your executable file "grompp" or "grompp_d", then you need to change your ".bashrc" file on your sytem to make it work this way. For doing this you need to have root permission. If this is the case check below on how to change the ".bashrc" profile.

    Now you make sure that you exit from the root by typing the next command.
    exit

Now what ever the folder you are in, try typing something like "gr" or "gro" at the command prompt and press the tab button. You should immediately see either "grompp" or "grompp_d" depending on your compilation precision style. For now don't worry about input file for this application and hit the enter button once you have one of these two names next to your command prompt. If you see something ( I guess I should say not something but lot) about Gromacs, that's good. Which means Gromacs is successfully installed on your system. I guess I should say that if you see one of two names "grompp" or "grompp_d", then Gromacs is successfully installed on your system. Anyway just hit the enter button and see what is says about Gromacs. At the end of that message, there will be some thing saying that there is an error. Don't worry about it. It's because we haven't given any file as input to Gromacs executable to run.

So after all this, if you have successfully installed Gromacs on your system, then you are good to go. I mean you are ready to start simulations with Gromacs. Otherwise if you haven't had success with installation and you have few problems in installing it and don't know how to figure them out, try to drop me an email at smanchu@uvm.edu and I would be more than happy to help you. Good luck.
Changing ".bashrc" file

Some times because of what ever reasons you don't see anything at your command prompt even after typing some part of name and pressing the tab. It doesn't display the full name of executable. Then you need to change the .bashrc file to get the full name of the executable when ever you type in part of the name and press the tab. For doing this you need to have root permission. You can always try to do this with out having permission. Some times it works.

    cd
    su   (for Linux)
    sudo  -s   (for Mac)
    emacs  .bashrc   (This opens the file. If you already have it, you see some commands on this file. If you already don't have this file on your system, then it just shows up empty.)
    PATH=/usr/local/gromacs:$PATH;  export  PATH

Most of the times, emacs doesn't open a separate window, but on the screen it self. So try to change the file on the screen and save it before quitting. Type the line (4) in to the file and press "control x" and then "control c" to quit. It will ask you to save or not before quitting. Simply put "y" for yes and hit enter. If you are on linux, then you get separate window. Then you can simply use GUI buttons on the toolbar at the top like cut, paste (yank), copy, etc. (By the way if you want to know how to install emacs editor with X-window display, which means you get separate window when ever you open something with emacs, keep checking this website. I am going to write it here on my website pretty soon). That's it. The file is saved and the link is created to executable file by telling the system the path to the location of the executable file. When you try to type, for example "grom" and press tab, system will right away start looking in these folders and it something matches with this, it will give the full name next to commnad prompt. Don't forget to exit from the root.

In the end I request you to report me at smanchu@uvm.edu the errors, in case you find any, with installation commands on this page.

[hojy]

باسلام
منم gromacs رو از ترمینال نصب گردم اما وقتی تو ترمینال مینویسم gromacs برنامه اجرا نمیشه!

[کیان]

چه پیغامی میده؟

[دانیال بهزادی]

اجرا نمی‌شه خیلی کلمه‌ی بی‌معنی‌ایه. بالخره چه اتّفاقی می‌افته دیگه! تا نگی چه اتّفاقی می‌افته این‌جا کسی علم غیب نداره که بدونه

[ahmadubuntu]

با سلام خدمت دوستان
من مراحل نصب رو طبق دستوری که در این لینک بود

http://www.cems.uvm.edu/~smanchu/gromacs_installation.html

تا مرحله 7 نصب پیش رفتم و فکر کنم که نرم افزار نصب شده البته این پیامی که تو ترمینال میاد

GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run "make tests" now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue "make links" now.
make[3]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'
make[1]: Leaving directory `/home/mohsen/Desktop/gromacs-3.3.3'

احتمالا باید خطهای زیر یا مشابهشون رو به فایل bashrc./~ اضافه کنی

کد: [انتخاب]

export PATH=$PATH:/usr/local/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:usr/local/lib

[hojy]

چه پیغامی میده؟

برا نصب میگه:
sudo apt-get install gromacs
Reading package lists... Done
Building dependency tree       
Reading state information... Done
gromacs is already the newest version.
واسه اجرا هم:
gromacs
gromacs: command not found
با سپاس از توجهتون!

[دانیال بهزادی]

خب برای نصب می‌گه که قبلا نصب شده
برای اجرا هم می‌گه اسم دستورش gromacs نیست و چیز دیگه‌ایه. مستنداتش رو بخون ببین چیه