APBS 1.5 binary installed, doesn't run multiple tthreads! about apbs

[keith923]

Hi Naty, Given that you are setting LD_LIBRARY_PATH, I'm assuming that you are on a linux box. Can you tell the distribution and version? It would also be helpful if you let me know how you have determined that it's running with a single thread. Thanks, - Keith From: Naty Clementi <[email protected]> Reply-To: Electrostatics/apbs-pdb2pqr <[email protected]> Date: Thursday, June 8, 2017 at 12:13 PM To: Electrostatics/apbs-pdb2pqr <[email protected]> Cc: Subscribed <[email protected]> Subject: [Electrostatics/apbs-pdb2pqr] APBS 1.5 binary installed, doesn't run multiple tthreads! (#476) I recently download the binary from the 1.5 version and after fixing the LD_LIBRARY_PATH, I was able to run a case. However it doesn't run in multiple threads. The same input file, runs in multiple thread in a 1.4.1 version I had installed. I tried to install the 1.5 binary in different machines and I always get the same problem. It only runs in 1 thread. Any ideas on what can be causing this? For the record, I have 1 processor with 4 physical cores (hyperthreading 8) . The input file looks like: read mol pqr built_parse.pqr end # LYSOZYME SOLVATION ENERGY -- SOLVATED STATE elec name lys-solv mg-manual dime 257 161 257 glen 50 40 50 # glen 69.43 61.38 77.82 gcent mol 1 mol 1 lpbe bcfl mdh ion charge 1 conc 0.15 radius 2.0 ion charge -1 conc 0.15 radius 2.0 pdie 4.0 sdie 80.00 chgm spl2 srfm mol srad 1.4 swin 0.3 sdens 50.0 temp 300.00 calcenergy total calcforce no end # LYSOZYME SOLVATION ENERGY -- REFERENCE STATE elec name lys-ref mg-manual dime 257 161 257 glen 50 40 50 # glen 69.43 61.38 77.82 gcent mol 1 mol 1 lpbe bcfl mdh ion charge 1 conc 0.00 radius 2.0 ion charge -1 conc 0.00 radius 2.0 pdie 4.0 sdie 4.00 chgm spl2 srfm mol srad 1.4 swin 0.3 sdens 50.0 temp 300.00 calcenergy total calcforce no end # Lysozyme solvation energy print elecEnergy lys-solv - lys-ref end quit — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://github.com/Electrostatics/apbs-pdb2pqr/issues/476>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AGGzFDiD26vXjTlEyTQdS4eg0bcqwV2nks5sCEffgaJpZM4N0gI->.

[ncclementi]

Hi Keith,
Yes you are right I'm on a linux distribution, precisely I'm on Ubuntu 16.04.
What I did to determine the single thread was by launching htop in a separate terminal and looking how the cores were working. When I used the old version (apbs 1.4.1) all of them cores are at 100% while with the new version only one. Besides I time the runs and are slower.

I also tried doing export OMP_NUM_THREADS=4 and still not work. any clue what can be going on?

[keith923]

Thanks for the additional information. We'll have to dig into this a bit. Thanks for your patience. - Keith From: Naty Clementi <[email protected]> Reply-To: Electrostatics/apbs-pdb2pqr <[email protected]> Date: Thursday, June 8, 2017 at 12:50 PM To: Electrostatics/apbs-pdb2pqr <[email protected]> Cc: "Star, Keith" <[email protected]>, Comment <[email protected]> Subject: Re: [Electrostatics/apbs-pdb2pqr] APBS 1.5 binary installed, doesn't run multiple tthreads! (#476) Hi Keith, Yes you are right I'm on a linux distribution, precisely I'm on Ubuntu 16.04. What I did to determine the single thread was by launching htop in a separate terminal and looking how the cores were working. When I used the old version (apbs 1.4.1) all of them cores are at 100% while with the new version only one. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://github.com/Electrostatics/apbs-pdb2pqr/issues/476#issuecomment-307208650>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AGGzFDLI7Zr8iHkNBLjBrmNMCBsDyoDDks5sCFBvgaJpZM4N0gI->.

[ncclementi]

Thanks for the reply and looking forward to know what is going on :)

[kozlac]

@ncclementi The reason the current version is not multithreading is that the compiler used to have multi-threading enabled by default which is not the case in newer versions. What you can do is compile APBS from source and enable multi-threading. If you need assistance doing this I'll be happy to help you.

[ncclementi]

@kozlac Are you guys planning on release a multi-thread binary version? I tried to build from source couple of times and I haven't been successful, and had troubles following the instructions since they are spread out, some in the master branch and others in the 1.4.1. In the build that is in master doesn't mention that you need to compile fetk, I found the instructions in the 1.4.1 branch but when I try to build I get always this error:

configure: error: GAMer libraries OR headers missing ...EXITING ON ERROR
make: *** No rule to make target 'install'.  Stop.
~/apbs/apbs-pdb2pqr/apbs/linux/fetk
---------------------- FETK-BUILD: STOPPING ----------------------

My steps so far were:

1- Clone the repo
2- git submodule init
3- git submodule update
4- In apbs-pdb2pqr/apbs --- > mkdir linux ----> cd linux
4- Copy the fetk folder that is in externals in the linux dir
5- ./fetk-build maloc punc gamer mc

[wleagle]

I cannot run apbs1.5 in multi-threading mode either. I have tried apbs1.4.2 and 1.5, both of them run in a single cpu core. Then I have tried to compile apbs 1.5 from the source, with the command "make -jN", or using Ninja. None of these methods work.

[kozlac]

Hi @wleagle, are you downloading the binaries from Sourceforge or GitHub? Also, on what platform are you trying to build from source?

[wleagle]

Hi! I download the binary from sourceforge, but the source code is cloned from Github. I built it on ubuntu 18.04, using cmake and make -jN.

…

On Fri, Jul 27, 2018 at 12:54 AM, Juan ***@***.***> wrote: Hi @wleagle <https://github.com/wleagle>, are you downloading the binaries from Sourceforge or GitHub? Also, on what platform are you trying to build from source? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/Electrostatics/apbs-pdb2pqr/issues/476#issuecomment-408163321>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Anw3JA1CCkQJUAEJSt8LZBhWuNdnT-maks5uKfQtgaJpZM4N0gI-> .

[kozlac]

@wleagle , I'll check the binaries in Sourceforge. In the meantime, there are binaries here in GitHub that should be multi-threading. Also, to build from source, you need to also initialize and update the submodules (via command git submodule init and git submodule update) after cloning the repo. Most likely the build is failing for this reason.

Once you have updated the submodules, you can then run cmake (pass -DENABLE_OPENMP flag to use threading) and then make. Some times the build fails when using the -jN option. If that happends, try to run just make with no flags.

Hopefully, this solves the issue. Please let me know if I can help any further. Thanks!!

[wleagle]

Thank you. I didn't notice the ENABLE_OPENMP section in cmakelist. I will try this.

…

On Sat, Jul 28, 2018, 00:18 Juan ***@***.***> wrote: I'll check the binaries in Sourceforge. In the meantime, there are binaries here <https://github.com/Electrostatics/apbs-pdb2pqr/releases> in GitHub that should be multi-threading. Also, to build from source, you need to also initialize and update the submodules (via command git submodule init and git submodule update) after cloning the repo. Most likely the build is failing for this reason. Once you have updated the submodules, you can then run cmake (pass -DENABLE_OPENMP flag to use threading) and then make. Some times the build fails when using the -jN option. If that happends, try to run just make with no flags. Hopefully, this solves the issue. Please let me know if I can help any further. Thanks!! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/Electrostatics/apbs-pdb2pqr/issues/476#issuecomment-408468003>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Anw3JGcB84J2KqfZlK99yvtRSzvLGTCkks5uKz1GgaJpZM4N0gI-> .

[sobolevnrm]

@intendo - can you please look into this given that you are upgrading the cmake setup

[intendo]

By default, the ENABLE_OPENMP is turned on in CMake so the resulting binaries will be multithreaded.

[namus]

By default, the ENABLE_OPENMP is turned on in CMake so the resulting binaries will be multithreaded.

For some reason, it is not the case for me. After running cmake, in the CMakeCache.txt file I found:
ENABLE_OPENMP:BOOL=OFF

I had to turn it ON to enable OpenMP. Also, the current binary downloaded from github doesn't run on multiple threads as mentioned in the original issue. So I guess the issue still persists, but can be resolved by compilation from source code after enabling OpenMP manually as mentioned above.

[intendo]

This may have been a result of the complicated CMake build system with all the external dependencies. We have revamped the CMake build system to use pre-built versions of all the external dependencies with greatly reduces the complexity (and time) to build APBS.