Incomplete configuration
Hi
I am trying to install OpenMS following the instructions at http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/install_linux.html.
I have run the following commands:
sudo apt-get install build-essential cmake autoconf patch libtool automake
sudo apt-get install qt4-default libqtwebkit-dev
sudo apt-get install libeigen3-dev libwildmagic-dev \
libxerces-c-dev libboost-all-dev libsvn-dev libgsl-dev libbz2-dev
# use from contrib for compatibility: SEQAN ; COINOR; ZLIB ; WILDMAGIC
# Assuming you are in ~/Development
git clone https://github.com/OpenMS/contrib.git
mkdir contrib-build
cd contrib-build
cmake -DBUILD_TYPE=LIST ../contrib
cmake -DBUILD_TYPE=SEQAN ../contrib
cmake -DBUILD_TYPE=WILDMAGIC ../contrib
cmake -DBUILD_TYPE=EIGEN ../contrib
All these commands work fine, but the next one does not work:
cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 ../contrib
I get the error:-- Configuring incomplete, errors occurred!
See also "/home/gcefalu/Development
Is it possible that I m missing some linux library?
CMakeOutput.log
I am trying to install OpenMS following the instructions at http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/install_linux.html.
I have run the following commands:
sudo apt-get install build-essential cmake autoconf patch libtool automake
sudo apt-get install qt4-default libqtwebkit-dev
sudo apt-get install libeigen3-dev libwildmagic-dev \
libxerces-c-dev libboost-all-dev libsvn-dev libgsl-dev libbz2-dev
# use from contrib for compatibility: SEQAN ; COINOR; ZLIB ; WILDMAGIC
# Assuming you are in ~/Development
git clone https://github.com/OpenMS/contrib.git
mkdir contrib-build
cd contrib-build
cmake -DBUILD_TYPE=LIST ../contrib
cmake -DBUILD_TYPE=SEQAN ../contrib
cmake -DBUILD_TYPE=WILDMAGIC ../contrib
cmake -DBUILD_TYPE=EIGEN ../contrib
All these commands work fine, but the next one does not work:
cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 ../contrib
I get the error:-- Configuring incomplete, errors occurred!
See also "/home/gcefalu/Development
Is it possible that I m missing some linux library?
CMakeOutput.log
ASKER
This time I used cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=1 ../contrib and it worked. Please see attached file. So what is the difference between 1 and 4?
Thank you for your help
Thank you for your help
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ASKER
Thanks. I will contact OpenMS and let them know.
ASKER
Hi,
I am getting an error pointing to a bug when I run the command make during Configuring and building OpenMS/TOPP at http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/install_linux.html
Please see below.
c++: internal compiler error: Killed (program cc1plus);Please submit a full bug report,;with preprocessed source if appropriate.;See <file:///usr/share/doc/gcc
It is a C++ compiler error. How could I fix this?
I am getting an error pointing to a bug when I run the command make during Configuring and building OpenMS/TOPP at http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/install_linux.html
Please see below.
c++: internal compiler error: Killed (program cc1plus);Please submit a full bug report,;with preprocessed source if appropriate.;See <file:///usr/share/doc/gcc
It is a C++ compiler error. How could I fix this?
I'd submit this error to the OpenMS project + ask for assistance.
Likely someone associated with OpenMS dev will now the answer instantly.
Likely someone associated with OpenMS dev will now the answer instantly.
ASKER
Hi,
It seems that the software consumes a lot of memory during installation. I had to increase the memory in my virtual machine to 4GB. Finally I have decided to install the program in a real ubuntu machine. Now, I am using Dell's NUC with 16 MG of memory. I know it has an intel quad processor, but I do not understand much about that. When I run the command above I can use 4 instead of 1 and it runs well to completion. I will study more carefully what makes the difference.
It seems that the software consumes a lot of memory during installation. I had to increase the memory in my virtual machine to 4GB. Finally I have decided to install the program in a real ubuntu machine. Now, I am using Dell's NUC with 16 MG of memory. I know it has an intel quad processor, but I do not understand much about that. When I run the command above I can use 4 instead of 1 and it runs well to completion. I will study more carefully what makes the difference.
ASKER
Now , I have to write a path in the .bashrc file and when I type sudo vi .bashrc I get an empty file. Is this supposed to be this way and I can just add my path or is there any thing going on?
Marking my solution as best.
Poster seems to have fixed problem + started a new question.
Poster seems to have fixed problem + started a new question.
ASKER
The question can be closed. I do not see a button on the web page to close the question. Thank you.
Using multiple jobs scrambles output of many steps, making debugging difficult.
Also the log you posted did not contain the Configuring incomplete message you mention.
So... Rebuild + post all commands + all output + your build log.