building spack

[abidmalikwaterloo]

Then edit ~/.spack/compilers.yaml (on Ubuntu, at least, it’s in ~/.spack/linux/compilers.yaml) and add /usr/bin/gfortran for both f77 and fcc

---

I did all the steps. could not find compilers.yaml on my Ubuntu machine

[jychoi-hpc]

Just found that we need to execute the following line: spack compilers to create compilers.yaml initially if there is nothing.

I have updated the document too.

[abidmalikwaterloo]

@jychoi-hpc Does Spack takecare of all dependencies?

[abidmalikwaterloo]

@jychoi-hpc The following doesn't work

spack install savanna@develop

getting the following

spack install savanna@develop No command 'spack' found, did you mean: Command 'pack' from package 'liballegro4-dev' (universe) Command 'cpack' from package 'cmake' (main) Command 'apack' from package 'atool' (universe) Command 'slack' from package 'slack' (universe) Command 'mpack' from package 'mpack' (universe) Command 'spock' from package 'python-sardana' (universe) Command 'ipack' from package 'exult-studio' (multiverse) Command 'spark' from package 'spark' (universe) spack: command not found

[abidmalikwaterloo]

@jychoi-hpc

suggestion:

Add the following before "spack install savanna@develop"

EXPORT PATH:$PATH:~/spack/bin

[abidmalikwaterloo]

==> 'cmake' '/home/amalik/spack/var/spack/stage/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/ffs-1.1.1' '-DCMAKE_INSTALL_PREFIX:PATH=/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE' '-DCMAKE_INSTALL_RPATH:STRING=/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/lib64:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-atl-2.1-obzod3knr3iesegnhm62r4xjvelztdvq/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-cercs-env-1.0-mi7osffjati4xggftwl3n5pfg3coxhed/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-dill-2.1-ryxlbxp575svrnzdp5liabfuxvhttge2/lib' '-DENABLE_TESTING=0' '-DTARGET_CNL=1' '-DBUILD_SHARED_STATIC=STATIC' -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /home/amalik/spack/lib/spack/env/gcc/gcc -- Check for working C compiler: /home/amalik/spack/lib/spack/env/gcc/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/amalik/spack/lib/spack/env/gcc/g++ -- Check for working CXX compiler: /home/amalik/spack/lib/spack/env/gcc/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of double -- Check size of double - done -- Check size of float -- Check size of float - done -- Check size of int -- Check size of int - done -- Check size of off_t -- Check size of off_t - done -- Check size of long -- Check size of long - done -- Check size of long double -- Check size of long double - done -- Check size of long long -- Check size of long long - done -- Check size of size_t -- Check size of size_t - done -- Looking for socket -- Looking for socket - found -- Could NOT find BISON (missing: BISON_EXECUTABLE) -- Found FLEX: /usr/bin/flex (found version "2.5.35") CMake Error at CMakeLists.txt:103 (BISON_TARGET): Unknown CMake command "BISON_TARGET".

-- Configuring incomplete, errors occurred!

[kshitij-v-mehta]

Looks like you need to install bison on your machine using the package manager

[ianfoster]

Dear Abid:

I recommend following the instructions at https://github.com/CODARcode/Example-Heat_Transfer https://github.com/CODARcode/Example-Heat_Transfer, as they include installing Bison, etc.

Regards — Ian

On Jul 20, 2017, at 8:41 AM, abidmalik1967 notifications@github.com wrote:

==> 'cmake' '/home/amalik/spack/var/spack/stage/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/ffs-1.1.1' '-DCMAKE_INSTALL_PREFIX:PATH=/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE' '-DCMAKE_INSTALL_RPATH:STRING=/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/libffs-1.1.1-u7dg3js7lh4phsuusb7txg2m7dxx3n7w/lib64:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-atl-2.1-obzod3knr3iesegnhm62r4xjvelztdvq/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-cercs-env-1.0-mi7osffjati4xggftwl3n5pfg3coxhed/lib:/home/amalik/spack/opt/spack/linux-ubuntu14-x86_64/gcc-4.8/gtkorvo-dill-2.1-ryxlbxp575svrnzdp5liabfuxvhttge2/lib' '-DENABLE_TESTING=0' '-DTARGET_CNL=1' '-DBUILD_SHARED_STATIC=STATIC' -- The C compiler identification is GNU 4.8.4 -- The CXX compiler identification is GNU 4.8.4 -- Check for working C compiler: /home/amalik/spack/lib/spack/env/gcc/gcc -- Check for working C compiler: /home/amalik/spack/lib/spack/env/gcc/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /home/amalik/spack/lib/spack/env/gcc/g++ -- Check for working CXX compiler: /home/amalik/spack/lib/spack/env/gcc/g++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of double -- Check size of double - done -- Check size of float -- Check size of float - done -- Check size of int -- Check size of int - done -- Check size of off_t -- Check size of off_t - done -- Check size of long -- Check size of long - done -- Check size of long double -- Check size of long double - done -- Check size of long long -- Check size of long long - done -- Check size of size_t -- Check size of size_t - done -- Looking for socket -- Looking for socket - found -- Could NOT find BISON (missing: BISON_EXECUTABLE) -- Found FLEX: /usr/bin/flex (found version "2.5.35") CMake Error at CMakeLists.txt:103 (BISON_TARGET): Unknown CMake command "BISON_TARGET".

-- Configuring incomplete, errors occurred!

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[abidmalikwaterloo]

fixed it. I think I missed the step for bison.

[abidmalikwaterloo]

@kshitij-v-mehta @jychoi-hpc

I ran the workflow as per instruction on the github. I am getting segmentation error due to "The connection is being refused.. errno 111"..

[mw70]

@abidmalik1967 Could you clarify what exactly is segfaulting? Since it's saying it's a connection, I'm assuming it isn't in the build environment, and you are trying to run the configuration somehow. Which transport are you using? Which of the swift workflows?

[abidmalikwaterloo]

@mw70 : I am attaching a file showing the errors.

out.txt

I used spack to build the savanna and then used run-workflow.sh script in the heat transfer to run the workflow. By default it takes "FLEXPATH" as transport. I am testing it on my local linux machine.

[kshitij-v-mehta]

Could you ensure you have enabled the FLEXPATH method in your xml file?

[abidmalikwaterloo]

I am attaching the file:

heat_transfer.txt

The other transports (MPI and dataspaces) are not being used. I am only using FLEXPATH.

[jychoi-hpc]

I cannot find any clue from your logs. Do you mind try the followings?

1. Rebooting your vm (if you use a VM)
2. Check if there is any remaining processes (ps -ef | grep mpi)
3. Uninstall and install savanna@develop and try again

[mw70]

@abidmalik1967 A quick response from Greg Eisenhauer -- error 111 means "connection refused". Could you check whether you have firewalls turned on for your local machine? The default connection used by Flexpath is TCP, since that is supported most everywhere, but if you have firewalls blocking the port, it won't work.

The segfault is potentially a separate issue, but it may be that there's some failed cleanup in the case that connection was refused as opposed to simply being not available. In which case fixing the fire wall should fix everything.

[abidmalikwaterloo]

@jychoi-hpc @mw70 It works with dataspaces.. Let me look into it further. Else I will install it again.

[abidmalikwaterloo]

@jychoi-hpc @mw70 able to run it on a Linux machine and a virtual machine. There was a problem in the BNL Linux machine's configuration which was breaking the run of the heat flow example.

[abidmalikwaterloo]

@jychoi-hpc @kshitij-v-mehta Does savanna run with MPI? I can run it with FLEXPATH and Dataspaces ( using cheetah).

[kshitij-v-mehta]

I believe it was tested manually and did run successfully.

[mw70]

@abidmalik1967 Just a reminder that the MPI Adios method is an abbreviation of MPI-IO -- it does not directly connect using MPI, but instead uses MPI-IO files as an intermediate connection. So it does work, but the workflow it uses is slightly different from the one in-memory connection methods.

[abidmalikwaterloo]

@jychoi-hpc @kshitij-v-mehta .. When I tried ./runworkflow.sh 16 MPI, it didn't work. I made changes in *.xml files before running. Did anyone try it using cheetah?

[jychoi-hpc]

"MPI" method has been added recently. Can you try again after uninstalling and installing savanna@develop?

The most recent version of Heat transfer code will have git hash "df8112b".

On Jul 28, 2017, at 10:17 AM, abidmalik1967 notifications@github.com wrote:

@jychoi-hpc @kshitij-v-mehta .. When I tried ./runworkflow.sh 16 MPI, it didn't work. I made changes in *.xml files before running. Did anyone try it using cheetah?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[abidmalikwaterloo]

@jychoi-hpc It worked. I noticed that the framework worked well with Ubuntu 16 and crashed with Ubuntu 14.