HPC 관련 내용 정리

CDO download site : https://code.zmaw.de/projects/cdo

cdo-1.5.6.1 설치 Bug 관련

### 오류 내용  ###

pipe.c(174): error: incomplete type is not allowed

    struct timespec time_to_wait;

time_to_wait 오류는 CDO 1.5.4 이후에 발생

해결 방법 : src 폴더에 pipe.c 선언 수정

- 변경 전 : #include <time.h> 

- 변경 후 : #include <sys/time.h> 

# Tachyon 2차 설치 방법( intel 11.1 compiler, openmpi 1.4.2 MPI 사용의 경우)

$ ./configure --prefix={설치 경로} --with-netcdf=/applic/compilers/intel/11.1/applib1/NETCDF4 \

   --with-hdf5=/applic/compilers/intel/11.1/applib1/HDF5

$ make

$ make install

module load compiler/pgi-9.0-4 mpi/mvapich-1.2.0

(1) sundials-2.3.0

$ tar xvzf sundials-2.3.0.tar.gz

$ cd sundials-2.3.0

$ ./configure --prefix=/home01/sunlsy/sundials

$ make

$ make install

(2) ParMetis-3.0

$ tar xvzf ParMetis-3.0.tar.gz

$ cd ParMetis-3.0

$ make

$ mkdir include

$ mkdir lib

$ cp *.h include

$ cp *.a lib

(3) petsc-3.1-p5

$ tar xvzf petsc-3.1-p5.tar.gz

$ cd petsc-3.1-p5

$ ./configure --with-sundials-dir=/home01/sunlsy/sundials \

  --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 \

  --with-parmetis-dir=/home01/sunlsy/ParMetis-3.0 \

  --download-superlu_dist=/home01/sunlsy/superlu_dist_2.4.tar.gz \

  --with-blas-lapack-dir=/applic/compilers/pgi/linux86-64/9.0-4/applib1/LAPACK

$ make PETSC_DIR=/home01/sunlsy/petsc-3.1-p5 PETSC_ARCH=linux-gnu-c-debug all

$ vi /home01/sunlsy/petsc-3.1-p5/linux-gnu-c-debug/conf/petscvariables

  PCC와 PCC_LINKER를 수정해 주세요.

  수정 전 : PCC = mpicc

  PCC_LINKER = mpicc

  수정 후 : PCC = mpicxx

  PCC_LINKER = mpicxx

(4) 환경설정

$ vi ~/.bashrc

아래 내용을 마지막에 추가해주세요.

export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/home01/sunlsy/sundials/lib:\

/home01/sunlsy/petsc-3.1-p5/linux-gnu-c-debug/lib:/home01/sunlsy/ParMetis-3.0/lib"

$ source ~/.bashrc

기본 환경 설정은 module load 로 설정해서 사용

$ module load compiler/gcc-4.4.6 mpi/openmpi-1.4.3

$ export LD_LIBRARY_PATH=/applic/wa/PYTHON/2.7.3/lib:$LD_LIBRARY_PATH

$ export PATH=/applic/wa/PYTHON/2.7.3/bin:$PATH

$ tar xvzf pcre-8.21.tar.gz 

$ cd pcre-8.21

$ ./configure --prefix=/home01/sunlsy/applib 

$ make

$ make install

$ cd ..

$ tar xvzf boost_1_54_0.tar.gz 

$ cd boost_1_54_0

$ vi bootstrap.sh

    PREFIX=/home01/sunlsy/applib

$ ./bootstrap.sh

$ ./b2 install --prefix=/home01/sunlsy/applib  

$ cd ..

$ tar xvzf sqlite-autoconf-3080002.tar.gz

$ cd sqlite-autoconf-3080002

$ ./configure --prefix=/home01/sunlsy/applib 

$ make

$ make install

$ cd ..

$ tar xvzf libantlr3c-3.2.tar.gz

$ cd libantlr3c-3.2

$ ./configure --prefix=/home01/sunlsy/applib --enable-64bit

$ make

$ make install

$ cd /home01/sunlsy/desmond-sourcecode

$ tar xvzf Desmond-3.4.0.2.tar.gz

$ cd Desmond-3.4.0.2

$ cp share/user-conf.sample.py share/user-conf.py

$ vi share/user-conf.py

$ scons --user-conf=./share/user-conf.py install PREFIX=/home01/sunlsy/Desmond-3.4.0.2

## sample run test

$ export DESMOND_PLUGIN_PATH=/home01/sunlsy/Desmond-3.4.0.2/lib/plugin

$ /home01/sunlsy/Desmond-3.4.0.2/bin/desmond \

--include /home01/sunlsy/Desmond-3.4.0.2/share/samples/dhfr.cfg \

--cfg boot.file=/home01/sunlsy/Desmond-3.4.0.2/share/samples/dhfr.dms \

--cfg mdsim.plugin.eneseq.name=dhfr.eneseq