•.♪*✿¨*•.*Uma's NoteBook...*

I found tunneling a remote gateway very slow and figured out a better way to work with synchronized projects. {This is very easy via ssh with -xy enabled on server and tunnel through x-window system (Xming For windows)}.
Login as
ssh -XY username@xx.yy.org in both the gateway and the machine.

I couldn't find a way to use Netbeans for remote C/C++/Fortran projects with a gateway yet. Below method is using Eclipse for linux or windows.

Files you have edit

Remote:

Your bashrc script or bash_profile - This is hidden in /home/username
Do : ll -a then vi bash_profile
Remote development by synchronized projects uses git. You need git installed on your remote machine. So we need to add the lines below to the end of your bash_profile script.

module load git
git config --global pack.windowMemory "100m"

git config --global pack.SizeLimit "100m"

git config --global pack.threads "1"

Local:
Eclipse seem to support Git inherently. So we only need to install eclipse neon for parallel C/C++ development

Eclipse settings --------------------------------------------------------------------------------

Goto Window>Preferences>Add

Add your gateway as the first connection. Give the Host name and your username. ( equivalent to , ssh username@host.org etc). Connection name could be anything you want. Here I set it as 'xcams gateway'.Choose password based connection, if you want to use a password. Then click finish.

Next we add the actual connection that is behind the gateway. Click Add a new connection again.

Give the connection name , host and username as before. Then click Advanced. In SSH Proxy settings, click Remote, and select the Gateway we created before. Now click finish.

Then click open button on the right hand side. This will open up the connection. If you didn't save your password, you have to enter the password now.

Next go to menu File>New>Other from the menu.

Then select Synchronized C/C++ projects from 'Other'.

Click Next. Then select the ssh connection (not the gateway).

Then select the Remote directory by clicking 'Browse' button.

Then Click the project folder you want to synchronize with.

Click ok. Give the Project name the same name as the project you selected.

Select the project type as GNU Auto Tools (This could be different depending on your project.) and select 'Empty project'.

**I had to do little bit more settings on windows to work because we need to support cross compilation with windows and our Linux based remote system. But it just works if you are using a linux machine.

Now choose to synchronize the project by right clicking on it unless auto sync is on by default. Screen shot is a windows system. But on Linux you need to specifically set it to sync. This may take a while if you have a rather large system on the remote machine.

** On windows 10 (This should be available on most windows OS)

goto control panel> Turn windows features on >

Click the check box saying, Windows subsystem for Linux

{This step is not necessary on Ubuntu}

credit: https://www.earthsystemcog.org/projects/cupid/proxyconnections and the great WWW!

******************************************************************************
More on setting up include paths for the remote synchronized project to run using remote machine:

(If needed, Click the link to goto eclipse help location which I'm quoting below )

"There are several places where include files are important to the editing, analyzing, building, and running of your program. A Synchronized Project mirrors the source files on the local machine as well as the remote target machine. Usually you edit locally, but build and run on the remote target. So this complicates things with respect to include files.

By default, a synchronized project uses the normal CDT discovery mechanism, which reads the local environment. To configure the new discovery elements, follow these instructions after creating a new synchronized project. Go to Project > Properties > C/C++ General > Preprocessor Include Paths, Macros etc. Make sure the remote configuration is selected at the top of the dialog. Under the Providers tab, deselect all CDT providers, except for "CDT User Setting Entries" if you would like to enter your own paths. Next, select the two Sync providers, "Sync GCC Build Output Parser" and "Sync GCC Builtin Compiler Settings." The latter provider runs a specially-crafted compiler command to get compiler-specific settings. It will run immediately after "OK" is selected. The former provider will execute simultaneously with builds. It intercepts the build output and attempts to find environment information. Thus, a build must be run before this provider is useful.

Now, make sure that indexing is enabled and invoke a remote build. In order for the build output parser to be useful, builds must produce verbose output. The method for setting up such a build varies per project, but see the Mozilla Project CDT setup page for a good example. Repeat these steps for each remote build configuration. For local configurations, both the standard CDT or new Sync providers should work. If you would like the environment to update automatically when build configurations are switched, go to Project > Properties > C/C++ General > Indexer and select "Use active build configuration" for "Build configuration for the indexer." The downside of this is that the indexer will run each time you switch configurations."

Here if you are connecting through a gateway remember to use the name of the ssh connection (2nd) instead of the full path name. Otherwise Eclipse tries to

login to the machine directly.

E.g: See below. Instead of using //nxxx.x.org/opt/../include use //ConnectionName/opt/../include when you set include files from remote location.

and add the lines below (logged into excl not newark yet.
. /opt/shared/sw/x86_64-unknown-linux-gnu/modules-tcl85/default/init/bash
module load modules
module use /opt/shared/sw/x86_64-unknown-linux-gnu/modulefiles/rhel6
#module use /opt/shared/sw/x86_64-unknown-linux-gnu/modulefiles/rhel7

then source or login again

. ~/.bashrc - sourcing bashrc: need to be in bash shell for this command

doesn't work for tcsh. no modules available in tcsh? why?

****If you are out of newark and load modules when u are in newark the paths are still there.Run config file in tcsh this way ; else it can't find modules

modules loaded in newark

d Modulefiles:
1) modules 3) boost/1.54.0-intel 5) python/2.7.11 7) hdf5/1.8.10-intel
2) m4/1.4.15 4) openssl/1.0.2c 6) openmpi/1.10.1-gnu

set env variables for games

export GMS_BUILD_DIR='/home/umunipala/gamess/gamess-kris-simgms
'
export GMS_TARGET=''
export GMS_PATH='/home/umunipala/gamess/gamess-kris-simgms
'
export GMS_FORTRAN='ifort'
export GMS_MATHLIB=''
set GMS_DDI_COMM=''

export GMS_TARGET=linux64
export GMS_PATH=/home/umunipala/gamess/gamess-kris-simgms

check if shell is interactive
[[ $- == *i* ]] && echo 'Interactive' || echo 'Not interactive'

----------------------------------------------4/13
Currently Loaded Modulefiles:
Currently Loaded Modulefiles: openssl is loaded by openmpi
1) modules 4) hdf5/1.8.10-intel 7) boost/1.60.0-gnu5
2) openssl/1.0.2c 5) openmpi/1.10.1-gnu 8) mkl/2013.5.192
3) python/2.7.11 6) m4/1.4.15 9) intel/2013.5.192

RUNNING CONFIG
>tcsh
>source ./config

Errors: gcc gfortran didn't show up . Logged in and out and its shown in
[umunipala@newark ~]$ which gcc
/usr/lib64/ccache/gcc

Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
Alas, your version of gfortran does not support REAL*16,
so relativistic integrals cannot use quadruple precision.
Other than this, everything will work properly.

MKL configuration
MKL version (or 'proceed')? proceed
Math library 'mkl' will be taken from /opt/intel/mkl/lib/intel64

---------------------------
Currently Loaded Modulefiles:
1) modules 6) hdf5/1.8.10-intel
2) mkl/2013.5.192 7) m4/1.4.15
3) intel/2013.5.192 8) boost/1.54.0-intel
4) openssl/1.0.2c 9) openmpi/1.10.1-gnu
5) python/2.7.11 10) mpich/3.1.2-gnu

mpich path::

set to::

/opt/shared/sw/x86_64-unknown-linux-gnu/mpich/3.1.2-gnu-rhel6

bin is here.

5) The subdirectory gamess/ddi contains a script 'compddi' to compile
the computer science support for parallel GAMESS, known as the
Distributed Data Interface (DDI).

There is one possible customization of 'compddi' that must be done
by hand-editing 'compddi', prior to running it. If your system's
number of cores per node or total number of nodes is large, reset
the defaults of MAXCPUS=8 and MAXNODES=128.

>did not change coz its only 8
>compddi : got error due to mpi

/opt/shared/sw/x86_64-unknown-linux-gnu/mpich/include/mpi.h

fixed it by changing mpi path to this(above)

compiled::
games>./compall

Thu Apr 13 15:17:10 EDT 2017
0.063u 0.018s 0:00.10 70.0% 0+0k 16+24io 0pf+0w
------------------- done with all compilations --------------------

linking failure : missing simgms.o

------------------4-17

**./comp simgms add line to compall
>./compal : no errors.
goto games/machines>
look in readme.unix step 7
goto games> run lked script to link libraries
./lked gamess 01 >& lked.log &

** change set SIMGMSLIBS line in lked script (this is not set for current user;hardcoded.)
set SIMGMSLIBS = "-L/home/kris/gamess/simgms/Debug -lsimgms -lstdc++ -L/home/kris/gamess/simgms/simint/lib -lsimint"
change the above to:

set SIMGMSLIBS = "-L/home/umunipala/gamess/gamess-kris-simgms/simgms/Debug -lsimgms -lstdc++ -L/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/lib -lsimint"

/home/umunipala/gamess/gamess-kris-simgms/simgms>>>
Readme says,
Add simgms.src to gamess source directory and use modified lked to link with gamess binary
/home/umunipala/gamess/gamess-kris-simgms/simgms/gamess_files>>
there is a lked and simgms.src
lked looks like the original config script

*****************************************Above might not be necessory
move simgms to source directory.
goto:
/home/umunipala/gamess/gamess-kris-simgms/simgms/gamess_files>>
cp simgms.src ../../source/simgms.src

ran the lked in this directory: asks to run config.
replaced original lked in games>> same error
./lked gamess 01 >& lked.log &

run /.compal
_____________________________________________________4/18 changed mkl path in config
lked errors, makefile in simgms/debug had licencing errors with intel
>Going back to configuring with gcc because the makefile is autogenerated.

/opt/intel/composer_xe_2013.5.192/mkl
changed modules

in readme.unix that is in machines folder says
If you are using the Ubuntu version of Linux, you will get better results by changing the top line of each script to read
#!/bin/tcsh in all the scripts below:
config compall comp lked rungms runall

run the compddi in gamess/ddi
run compall after going back to bash and loading modules.
reverted from tcsh to bash and changed to #!/bin/csh in compall

goto games/simgms/Debug> make -icpc=cc

ran ./lked gamess 01 >& lked.log & and still there is no libsimgms.a or .so
checked with find . -name libsimgms*
not available.

module load gcc
module load make
module load python/2.7.11
module load openmpi/1.10.1-gnu
module load hdf5/1.8.10-intel
module load boost/1.60.0-gnu5
module load mkl/2013.5.192
module load mpich/3.1.2-gnu

____________________4/24/17
changing makefiles in Debug folder

subdir.mk : contains wrong path

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 is mkl lib and they are shared/dynamic

-std=gnu++11 -lmkl_intel_ilp64 -lmkl_gnu_thread

/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64
setenv LD_LIBRARY_PATH /opt/intel/composer_xe_2013.5.192/mkl/lib/intel64:$LD_LIBRARY_PATH

-----------------------------4/26---------
fix intrinsics_avx.h error
________________________-approach 1--didn't work
goto /home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include/simint/vectorization
>>
current files here are:

intrinsics_avx512.h intrinsics_scalar.h vectorization.h
intrinsics_avx.h intrinsics_sse.h

>> Now adding headers..
change the header from <> to "immintrin.h" in intrinsics_avx.h

>>gcc libs
/opt/shared/sw/x86_64-unknown-linux-gnu/gcc/5.3.0-rhel6/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/include
-------------------------------approach 2-----------------

define your own macro like this in intrinsics_avx.h

#define _mm256_set_m128d(vh, vl) \
_mm256_insertf128_pd(_mm256_castpd128_pd256(vl), (vh), 1)

Instead #define SIMINT_GCC in intrinsics_avx.h

------------------------------------------------------------make o/p
[umunipala@newark Debug]$ make
Building file: ../simgms_init.cpp
Invoking: G++ Compiler
g++ -g -O -O1 -std=c++11 -L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 -libmkl_lapack95_lp64 -libmkl_intel_lp64 -libmkl_core -lmkl_gnu_thread -I/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include -DDEBUG -DMKL_ILP64 -MMD -MP -MF"simgms_init.d" -MT"simgms_init.d" -c -o "simgms_init.o" "../simgms_init.cpp"
In file included from /home/umunipala/gamess/gamess-kris-simgms/simgms/simint/incl
ude/simint/vectorization/vectorization.h:11:0,
from /home/umunipala/gamess/gamess-kris-simgms/simgms/simint/incl
ude/simint/ostei/ostei_config.h:3,
from /home/umunipala/gamess/gamess-kris-simgms/simgms/simint/incl
ude/simint/simint.h:5,
from ../simgms_init.h:3,
from ../simgms_init.cpp:3:
/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include/simint/vectorizati
on/intrinsics_avx.h: In function '__m256d simint_exp_vec4(__m256d)':
/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include/simint/vectorizati
on/intrinsics_avx.h:25:48: warning: AVX vector return without AVX enabled changes the ABI [-Wpsabi]
static inline __m256d simint_exp_vec4(__m256d x)
^
Finished building: ../simgms_init.cpp

Building file: ../simgms_math.cpp
Invoking: G++ Compiler
g++ -g -O -O1 -std=c++11 -L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 -libmkl_lapack95_lp64 -libmkl_intel_lp64 -libmkl_core -lmkl_gnu_thread -I/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include -DDEBUG -DMKL_ILP64 -MMD -MP -MF"simgms_math.d" -MT"simgms_math.d" -c -o "simgms_math.o" "../simgms_math.cpp"
../simgms_math.cpp:2:25: fatal error: mkl_lapacke.h: No such file or directory
compilation terminated.
---------------------------------
/opt/intel/composer_xe_2013.5.192/mkl????????????????? sometimes this path shows as available and sometimes not? why?
/opt/intel/composer_xe_2013.5.192/mkl/include
has mkl_lapack.h file
-----------------------------------------------------------

generated libsimint.a in libs and there is two more files simgms_init.d and simgms_init.o generated.

compiling lked script in main directory
./lked gamess 01 >& lked.log &

-------------------------------------------------current build error
gcc -mavx -g -O -O1 -std=c++11 -L/opt/intel/composer_xe_2013.5.192/mkl/lib/intel64 -libmkl_mc -libmkl_sequential -libmkl_gf_ilp64 -libmkl_avx -libmkl_lapack95_lp64 -libmkl_intel_lp64 -libmkl_core -lmkl_gnu_thread -I/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include -DDEBUG -DMKL_ILP64 -MMD -MP -MF"simgms_math.d" -MT"simgms_math.d" -c -o "simgms_math.o" "../simgms_math.cpp"
In file included from ../simgms_math.cpp:2:0:
../mkl_lapacke.h:32:23: fatal error: mkl_types.h: No such file or directory
compilation terminated.
subdir.mk:31: recipe for target 'simgms_math.o' failed
make: *** [simgms_math.o] Error 1

-------------------------------------
simgms/Debug>
got an error 'CBLAS_LAYOUT undeclared
fixed it with adding line typedef CBLAS_ORDER CBLAS_LAYOUT; /* this for backward compatibility with CBLAS_ORDER */
to simgms_math.cpp

Ran make in Debug folder.
This generated libsimgs.a

go up to main lked script

________________________________modified headers in simgms_math.cpp

added include files.
/opt/intel/composer_xe_2013.5.192/compiler/lib/intel64

./lked gamess 01 >& lked_may_1.log &

libs gcc
/opt/shared/sw/x86_64-unknown-linux-gnu/gcc/5.3.0-rhel6/lib64
added this line to simint.
define

look for files in /opt/intel/composer_xe_2013.5.192/compiler/lib/intel64

gcc -I/opt/intel/composer_xe_2013.5.192/compiler/include-L/opt/intel/composer_xe_2013.5.192/compiler/lib/intel64 __intel_ssse3_rep_memcpy
-----

added macro #define SIMINT_GC in simgms_init.cpp and simgms_oei.cpp --- not sure: bcoz it was mentioned in vectorization.h
---------------------may 1
copied all the header files from the Debug directory generated from the files like simgms_math, simgms_oie etc (which we in Debug )into the folder below.
Then added the bath in subdir.mk
-I/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include/simint/debug
./lked gamess 01 >& lked_may_1.log &

*** Run makefile from following directory:

/home/umunipala/gamess/gamess-kris-simgms/simgms/oed
changed ifort to gfortran in Makefile
FC=gfortran

This generates the libraries for oed

----------Edit lked script----------------------
in lked script CHANGE THIS LINE ADDING OED LIB

if($SIMGMS == true) then
set SIMGMSLIBS = "-L$GMS_BUILD_DIR/simgms/Debug -lsimgms -L$GMS_BUILD_DIR/simgms/oed -liboed -liboedlib -lstdc++ -L$GMS_BUILD_DIR/simgms/simint/lib -lsimint"
-liboed -liboedlib was wrong
Replace by -loed -loedlib

if($SIMGMS == true) then
set SIMGMSLIBS = "-L$GMS_BUILD_DIR/simgms/Debug -lsimgms -L$GMS_BUILD_DIR/simgms/oed -loed -loedlib -lstdc++ -L$GMS_BUILD_DIR/simgms/simint/lib -lsimint"
./lked gamess 01 >& lked_may_1.log &

changed file with wrong paths that were hardcoded
Debug/simgms_diagonalize.d

---------------------may 3---

changed linked order to simgms, simint ... etc

ran lked

./lked gamess 01 >& lked_may_3.log &

openmpi path is wrong in $PATH
rhe16 doesn't exist
available directory is:
/opt/shared/sw/x86_64-unknown-linux-gnu/openmpi

Errors in lked are from intel function calls from these files:
1. shell.h , there is no shell.c

/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/include/simint

change simint_config.h
remove #define SIMINT_INTEL and add #define SIMINT_GCC
now simint need to be compiled
how do we do this???
------------------------------------------------------may 5 ------------------

extracted and renamed simint version 7 to simint
created build directory in simint dir
First run cmake in the toplevel and this creates the subdirectory simint and the cmakelist there.

ran cmake command with avx
simint>> CC=gcc CXX=g++ cmake . -DSIMINT_VECTOR=avx

simgms/simint>> make
This builds all *.o objects
But its very slow.. next time try -j8. Then ran make all

[umunipala@newark simint]$ pwd
/home/umunipala/gamess/gamess-kris-simgms/simgms/simint
[umunipala@newark simint]$ make all DESTDIR=.
------------------------
Now we have to run cmake in the subdirectories examples and then in simint.

1)
now goto /siminit/examples>> run cmake
CC=gcc CXX=g++ cmake . -DSIMINT_VECTOR=avx -DCMAKE_INSTALL_LIBDIR=./lib -DCMAKE_INSTALL_INCLUDEDIR=./include

2)
now goto /siminit/simint>> and run cmake to build the library
Also create lib and include directories here and give them as cmake variables.

[umunipala@newark simint]$ pwd
/home/umunipala/gamess/gamess-kris-simgms/simgms/simint/simint

[umunipala@newark simint]$ CC=gcc CXX=g++ cmake . -DSIMINT_VECTOR=avx -DCMAKE_INSTALL_LIBDIR=./lib -DCMAKE_INSTALL_INCLUDEDIR=./include

added this line to the beginning of file CMakeLists in simgms/simgms dir before running cmake :
cmake_minimum_required(VERSION 3.3)

make
make all

libsimint.a is created in simint. copy this to simint/lib

-----------------------------
goto lked and run it.

./lked gamess 01 >& lked_may_5.log &
errors libmkl_gnu_thread.so: undefined reference to `omp_in_parallel' etc
added -lgomp to mkl Lib path

---------------5/26----------------
missing
#define SIMINT_GCC in the current buld from the new simgms version,in 'simgms_init.cpp'

•.♪✿¨•.Uma's NoteBook...

May 11, 2017

Build / Debug c/c++ synchronized projects behind ssh remote gateway via Eclipse ( Client-Server type)

May 9, 2017

REMOTE C/C++ through gateways using Eclipse

Remote gatway debugging without ssh tunneling

May 5, 2017

GAMESS build notes

May 3, 2017

Visustin :: Code Analyzer / Diagram generator

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