ArkoudaProject/community

pierce

@pierce314159

Arkouda v2022.05.05 was just released! Thanks to everyone who contributed!
https://github.com/Bears-R-Us/arkouda/releases/tag/v2022.05.05

Chris Long

@compiling-is-winning

Hi all, stupid questions as I haven't built Arkouda since January, both related to Apache Arrow (I assume for the new Parquet support):

1) On my Mac laptop, I've had no success building dependencies locally with “make install-deps”. However, I can get each of Arrow, HDF5, and ZeroMQ from Brew. I added a lines to Makefile.paths for the paths to /usr/local/Cellar for each of these. It compiles just fine, and I can run a single-locale Arkouda server with basic functionality. However, if I run “make test-all”, I get a bunch of failed tests related to parquet. So am I pointing Arkouda to the right place to build with Arrow via that line in Makefile.paths?

2) On Sherlock, I build hdf5 and zeromq fine with “make install-reps”. However, I get a CMake error when trying to build Arrow. Initially, the error was that it wasn’t finding Boost. So I installed a later version of CMake, but am now getting a errors to the effect that CMake is looking for modules in the wrong directory and cannot find CMAKE_ROOT. Has anyone else encountered this?

Brad Chamberlain

@bradcray

For #1, I have not tried to build Parquet / Arrow on my Mac but have not had to manually add paths to brew packages for other things. I guess my main thought there is whether some additional brew step is required to add the brew paths to your environment’s search path variables or the like? E.g., would a normal C compile find the headers and libraries without additional help? Some brew install steps ask you to add some lines to your .bashrc to enable them, though it’s been awhile since I’ve had to do one of those, so I’m not certain.

For the Parquet question, I’m tagging @bmcdonald3 who’s the resident expert.

I have not seen that specific cmake error you’re seeing, though in the plan-old Chapel context, I have seen cases where our build process will embed cmake paths into some sort of files, and I’ve had to do a fairly extensive clobber to clean things up and rebuild once I’ve switched cmake versions. I haven’t yet taken the time to figure out why that is, or whether our Makefiles could be updated to take care of it automatically. I wonder whether the same could be true with your Sherlock build as well, though the context is definitely different…?

pierce

@pierce314159

hey @compiling-is-winning, @Ethan-DeBandi99 says he'll sync with u about this tomorrow, but we think the failed tests might be solved by PR Bears-R-Us/arkouda#1392

Chris Long

@compiling-is-winning

@bradcray thanks! My guess is that it would. If I just run "which h5ls" (or something analogous for the zeromq and arrow dependencies) I get a path to a system directory that, on further inspection, contains a symbolic link to the directory in Cellar where it was installed with Brew. For the CMake issues on Sherlock, I will clobbering all of my existing installs later tonight

@pierce314159 cool, thanks! If I run "make test-all", I do indeed get one error in dataframe_test.py and two in io_test.py, with the same routines as mentioned in the PR you linked above

Chris Long

@compiling-is-winning

Looks like with "make test-chapel" I get one error with UnitTestParquetCpp

Michael Merrill

@mhmerrill

@compiling-is-winning i just checked in the PR that fixes the problem i think

pierce

@pierce314159

also @compiling-is-winning, do you have the ARKOUDA_SERVER_PARQUET_SUPPORT env variable set? You might need to run export ARKOUDA_SERVER_PARQUET_SUPPORT=trueand rebuild the server

Chris Long

@compiling-is-winning

@mhmerrill @pierce314159 thanks, that cleared up all but the dataframe_test issue with the Python tests on my Mac. Still fighting cmake on Sherlock

Michael Merrill

@mhmerrill

Anyone have a topic for today’s call?

Michael Merrill

@mhmerrill

Today's Arkouda Call will be further discussion of Radix sort structure and mason packages , are people ok with these topics?

Rajendra Prasad Patil

@rp98njit

Hi everyone,

I am trying to build arkouda
I am getting this error.

make: Entering directory /home/r/rp98/arkouda' make compile-arrow-cpp make[1]: Entering directory/home/r/rp98/arkouda'
g++ -O3 -std=c++11 -c /home/r/rp98/arkouda//src/ArrowFunctions.cpp -o /home/r/rp98/arkouda//src/ArrowFunctions.o -I/home/r/rp98/anaconda3/envs/arkouda/include -L/home/r/rp98/anaconda3/envs/arkouda/lib
In file included from /home/r/rp98/arkouda//src/ArrowFunctions.cpp:1:0:
/home/r/rp98/arkouda//src/ArrowFunctions.h:7:10: fatal error: arrow/api.h: No such file or directory

include <arrow/api.h>

      ^~~~~~~~~~~~~

compilation terminated.
make[1]: [compile-arrow-cpp] Error 1
make[1]: Leaving directory `/home/r/rp98/arkouda'
make: [/home/r/rp98/arkouda//src/ArrowFunctions.o] Error 2
make: Leaving directory `/home/r/rp98/arkouda'
(arkouda) login-1-57 arkouda-njit >:

Thank you in advance

Michael Merrill

@mhmerrill

@rp98njit we’ve got someone looking into it, I might have to do with a PR we merged yesterday which made Parquet/Arrow a non optional part of the build

Ethan-DeBandi99

@Ethan-DeBandi99

@mhmerrill /@rp98njit it definitely is related to that. I am looking to see what specifically is not configured to cause that.

@rp98njit Can you confirm a few things for me? Do you have the LD_LIBRARY_PATH environment variable set?

2 replies

Ethan-DeBandi99

@Ethan-DeBandi99

@rp98njit Also, have you run make install-arrow?

Ethan-DeBandi99

@Ethan-DeBandi99

Ok - I believe the issue is that arrow is not installed running make install-arrow should resolve this. I have added an issue to update our install documentation to reflect this

15 replies

Ethan-DeBandi99

@Ethan-DeBandi99

@rp98njit I created a bare bones conda environment to run the install in and make sure everything is functional. Here is the list of packages that need to be installed using conda before make install-arrow will run.

boost-cpp
snappy
thrift-cpp
re2
utf8proc

Please let me know if it gives you any additional problems after installing the packages listed above.

Ethan-DeBandi99

@Ethan-DeBandi99

Additionally, here is the command if using pip,
pip install boost snappy thrift re2 utf8proc

pierce

@pierce314159

Arkouda v2022.06.06 was just released! Thanks to everyone who contributed!
https://github.com/Bears-R-Us/arkouda/releases/tag/v2022.06.06

Michael Merrill

@mhmerrill

Today's Arkouda Weekly Call is cancelled.

Engin Kayraklioglu

@e-kayrakli

@/all In case you missed it, CHIUW is today and we just started. Just register here and hop in! https://hpe.zoom.us/meeting/register/tJEoc-2orzotH9QYrnGAJOIGveblfnGKtNw0 (Ooh, Brad is talking about Arkouda right now)

Rajendra Prasad Patil

@rp98njit

Hi all,
Thanks in advance.

How can I verify? I installed the chapel with the "LLVM=bundled" configuration.

Michael Merrill

@mhmerrill

@rp98njit you should put that question in the chapel gitter channel https://gitter.im/chapel-lang/chapel

pierce

@pierce314159

Arkouda v2022.06.13 was just released!
https://github.com/Bears-R-Us/arkouda/releases/tag/v2022.06.13

Michael Merrill

@mhmerrill

Anyone have a topic for today's Arkouda weekly call? https://github.com/Bears-R-Us/ArkoudaWeeklyCall

@/all Anyone have a topic for today's Arkouda weekly call? https://github.com/Bears-R-Us/ArkoudaWeeklyCall

Michael Merrill

@mhmerrill

@/all if no takers to today's call we will cancel, any takers...

@/all we will spend today's meeting talking about and recapping CHIUW.

pierce

@pierce314159

just circling back on @rp98njit's issue, it was resolved by running conda install -c conda-forge pyarrow

Zhihui Du

@zhihuidu

addEntry problem.
In my tests for a large graph amazon0601.txt, the st.addEntry function will be blocked somewhere after giving the following information
"2022-06-18:11:58:59 [ServerConfig] overMemLimit Line 202 INFO [Chapel] memory high watermark = 267023064 memory limit = 486862464614"
No error information is given. It seems that it enters into an infinite loop.

For small graphs, everything is good.

Any suggestions on solving this problem? Thanks!

Michael Merrill

@mhmerrill

@zhihuidu this message is printed when you allocate more memory that at any point before in the run. From the message it appears that you still have plenty of memory left. I don’t think the message is tied to the behavior you are seeing. Are you using standard Arkouda I/O to read in your data?

Zhihui Du

@zhihuidu

Thanks, Mike!
In the previous tests, I used writeln and it could not show output immediately.
After using the standard Arkouda I/O, I have located the position of the problem.
I am looking into the problem to see why a large graph will have an infinite loop.

Michael Merrill

@mhmerrill

@/all anyone have a topic for today's Arkouda Weekly Call?

Michael Merrill

@mhmerrill

@/all if there are no topics to discuss then we will cancel today call.

Michael Merrill

@mhmerrill

@/all would people be interested in me talking about a new/experimental way of interpreting arkouda array computation?

pierce

@pierce314159

Hi everyone! The Arkouda weekly call for today is canceled

Chris Long

@compiling-is-winning

Does Arkouda have a supported uint32 datatype? I don't see one here: https://bears-r-us.github.io/arkouda/autoapi/arkouda/dtypes/index.html?highlight=dtype#module-arkouda.dtypes

I ask because I'm currently working on a server-side algorithm that will require concatenating two integers (one a set element index, the other a hash index) into a single uint64 that will be used to seed a random number generator. So it would be easiest if both indices above were uint32's, though not necessarily a deal-breaker if not.

Michael Merrill

@mhmerrill

Not in memory but I think you can read and write 32-bit in file I/O. You should ask Bill about this.

There is really no reason to support it other than to conserve memory.

Chris Long

@compiling-is-winning

Thanks! I'm guessing a uint8 would suffice for the hash index (and looks to be supported), so I could probably just put in a check on the set element index to make sure that the concatenated value will still be representable as a uint64

I suppose that I could also use a Cantor pairing function, though I haven't thought this through much either

Chris Long

@compiling-is-winning

The pairing function would also give me an actual uniqueness guarantee (even though I expect that the number of hashes will be something small like 10 or less, so that this isn't a big issue in practice)

pierce

@pierce314159

Hi everyone! The meeting today is canceled since mike is on vacation. Hope everyone had a good 4th!

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include <arrow/api.h>