Hi Matthias, With a driver memory of 10GB, all operations were executed on CP, and I did observe that the version of reading FK as a vector and then converting it was faster, which took 8.337s (6.246s on GC) while the version of reading FK as a matrix took 31.680s (26.256s on GC).
For the distributed caching, I have re-run all scripts with the following Spark configuration --driver-memory 1G \ --executor-memory 100G \ --executor-cores 20 \ --num-executors 1 \ --conf spark.driver.maxResultSize=0 \ --conf spark.rpc.message.maxSize=128 \ And it seems that both versions have some problems. 1) Sum of FK in matrix form ``` FK = read($FK) print("Sum of FK = " + sum(FK)) ``` Worked as expected. Took 8.786s. 2) Sum of FK in matrix form, with checkpoints ``` FK = read($FK) if (1 == 1) {} print("Sum of FK = " + sum(FK)) ``` It took 89.731s, with detailed stats shown below. 17/05/08 13:15:00 INFO api.ScriptExecutorUtils: SystemML Statistics: Total elapsed time: 91.619 sec. Total compilation time: 1.889 sec. Total execution time: 89.731 sec. Number of compiled Spark inst: 2. Number of executed Spark inst: 2. Cache hits (Mem, WB, FS, HDFS): 1/0/0/0. Cache writes (WB, FS, HDFS): 0/0/0. Cache times (ACQr/m, RLS, EXP): 0.000/0.001/0.000/0.000 sec. HOP DAGs recompiled (PRED, SB): 0/0. HOP DAGs recompile time: 0.000 sec. Spark ctx create time (lazy): 0.895 sec. Spark trans counts (par,bc,col):0/0/0. Spark trans times (par,bc,col): 0.000/0.000/0.000 secs. Total JIT compile time: 5.001 sec. Total JVM GC count: 8. Total JVM GC time: 0.161 sec. Heavy hitter instructions (name, time, count): -- 1) sp_uak+ 89.349 sec 1 -- 2) sp_chkpoint 0.381 sec 1 -- 3) == 0.001 sec 1 -- 4) + 0.000 sec 1 -- 5) print 0.000 sec 1 -- 6) castdts 0.000 sec 1 -- 7) createvar 0.000 sec 3 -- 8) rmvar 0.000 sec 7 -- 9) assignvar 0.000 sec 1 -- 10) cpvar 0.000 sec 1 3) Sum of FK in vector form ``` FK_colvec = read($FK_colvec) FK = table(seq(1,nrow(FK_colvec)), FK_colvec, nrow(FK_colvec), 1e6) print("Sum of FK = " + sum(FK)) ``` Things really went wrong. It took ~10 mins. 17/05/08 13:26:36 INFO api.ScriptExecutorUtils: SystemML Statistics: Total elapsed time: 605.688 sec. Total compilation time: 1.857 sec. Total execution time: 603.832 sec. Number of compiled Spark inst: 2. Number of executed Spark inst: 2. Cache hits (Mem, WB, FS, HDFS): 1/0/0/0. Cache writes (WB, FS, HDFS): 0/0/0. Cache times (ACQr/m, RLS, EXP): 0.000/0.000/0.000/0.000 sec. HOP DAGs recompiled (PRED, SB): 0/1. HOP DAGs recompile time: 0.002 sec. Spark ctx create time (lazy): 0.858 sec. Spark trans counts (par,bc,col):0/0/0. Spark trans times (par,bc,col): 0.000/0.000/0.000 secs. Total JIT compile time: 3.682 sec. Total JVM GC count: 5. Total JVM GC time: 0.064 sec. Heavy hitter instructions (name, time, count): -- 1) sp_uak+ 603.447 sec 1 -- 2) sp_rexpand 0.381 sec 1 -- 3) createvar 0.002 sec 3 -- 4) rmvar 0.000 sec 5 -- 5) + 0.000 sec 1 -- 6) print 0.000 sec 1 -- 7) castdts 0.000 sec 1 Also, from the executor log, there were some disk spilling: 17/05/08 13:20:00 INFO ExternalSorter: Thread 109 spilling in-memory map of 33.8 GB to disk (1 time so far) 17/05/08 13:20:20 INFO ExternalSorter: Thread 116 spilling in-memory map of 31.2 GB to disk (1 time so far) ... 17/05/08 13:24:50 INFO ExternalAppendOnlyMap: Thread 116 spilling in-memory map of 26.9 GB to disk (1 time so far) 17/05/08 13:25:08 INFO ExternalAppendOnlyMap: Thread 109 spilling in-memory map of 26.6 GB to disk (1 time so far) Regards, Mingyang On Sat, May 6, 2017 at 9:12 PM Matthias Boehm <mboe...@googlemail.com> wrote: > yes, even with the previous patch for improved memory efficiency of > ultra-sparse matrices in MCSR format, there is still some unnecessary > overhead that leads to garbage collection. For this reason, I would > recommend to read it as vector and convert it in memory to an ultra-sparse > matrix. I also just pushed a minor performance improvement for reading > ultra-sparse matrices but the major bottleneck still exist. > > The core issue is that we can't read these ultra-sparse matrices into a CSR > representation because it does not allow for efficient incremental > construction (with unordered inputs and multi-threaded read). However, I > created SYSTEMML-1587 to solve this in the general case. The idea is to > read ultra-sparse matrices into thread-local COO deltas and finally merge > it into a CSR representation. The initial results are very promising and > it's safe because the temporary memory requirements are covered by the MCSR > estimate, but it will take a while because I want to introduce this > consistently for all readers (single-/multi-threaded, all formats). > > In contrast to the read issue, I was not able to reproduce the described > performance issue of distributed caching. Could you please double check > that this test also used the current master build and perhaps share the > detailed setup again (e.g., num executors, data distribution, etc). Thanks. > > Regards, > Matthias > > > On Thu, May 4, 2017 at 9:55 PM, Mingyang Wang <miw...@eng.ucsd.edu> wrote: > > > Out of curiosity, I increased the driver memory to 10GB, and then all > > operations were executed on CP. It took 37.166s but JVM GC took 30.534s. > I > > was wondering whether this is the expected behavior? > > > > Total elapsed time: 38.093 sec. > > Total compilation time: 0.926 sec. > > Total execution time: 37.166 sec. > > Number of compiled Spark inst: 0. > > Number of executed Spark inst: 0. > > Cache hits (Mem, WB, FS, HDFS): 0/0/0/1. > > Cache writes (WB, FS, HDFS): 0/0/0. > > Cache times (ACQr/m, RLS, EXP): 30.400/0.000/0.001/0.000 sec. > > HOP DAGs recompiled (PRED, SB): 0/0. > > HOP DAGs recompile time: 0.000 sec. > > Spark ctx create time (lazy): 0.000 sec. > > Spark trans counts (par,bc,col):0/0/0. > > Spark trans times (par,bc,col): 0.000/0.000/0.000 secs. > > Total JIT compile time: 22.302 sec. > > Total JVM GC count: 11. > > Total JVM GC time: 30.534 sec. > > Heavy hitter instructions (name, time, count): > > -- 1) uak+ 37.166 sec 1 > > -- 2) == 0.001 sec 1 > > -- 3) + 0.000 sec 1 > > -- 4) print 0.000 sec 1 > > -- 5) rmvar 0.000 sec 5 > > -- 6) createvar 0.000 sec 1 > > -- 7) assignvar 0.000 sec 1 > > -- 8) cpvar 0.000 sec 1 > > > > Regards, > > Mingyang > > > > On Thu, May 4, 2017 at 9:48 PM Mingyang Wang <miw...@eng.ucsd.edu> > wrote: > > > > > Hi Matthias, > > > > > > Thanks for the patch. > > > > > > I have re-run the experiment and observed that there was indeed no more > > > memory pressure, but it still took ~90s for this simple script. I was > > > wondering what is the bottleneck for this case? > > > > > > > > > Total elapsed time: 94.800 sec. > > > Total compilation time: 1.826 sec. > > > Total execution time: 92.974 sec. > > > Number of compiled Spark inst: 2. > > > Number of executed Spark inst: 2. > > > Cache hits (Mem, WB, FS, HDFS): 1/0/0/0. > > > Cache writes (WB, FS, HDFS): 0/0/0. > > > Cache times (ACQr/m, RLS, EXP): 0.000/0.000/0.000/0.000 sec. > > > HOP DAGs recompiled (PRED, SB): 0/0. > > > HOP DAGs recompile time: 0.000 sec. > > > Spark ctx create time (lazy): 0.860 sec. > > > Spark trans counts (par,bc,col):0/0/0. > > > Spark trans times (par,bc,col): 0.000/0.000/0.000 secs. > > > Total JIT compile time: 3.498 sec. > > > Total JVM GC count: 5. > > > Total JVM GC time: 0.064 sec. > > > Heavy hitter instructions (name, time, count): > > > -- 1) sp_uak+ 92.597 sec 1 > > > -- 2) sp_chkpoint 0.377 sec 1 > > > -- 3) == 0.001 sec 1 > > > -- 4) print 0.000 sec 1 > > > -- 5) + 0.000 sec 1 > > > -- 6) castdts 0.000 sec 1 > > > -- 7) createvar 0.000 sec 3 > > > -- 8) rmvar 0.000 sec 7 > > > -- 9) assignvar 0.000 sec 1 > > > -- 10) cpvar 0.000 sec 1 > > > > > > Regards, > > > Mingyang > > > > > > On Wed, May 3, 2017 at 8:54 AM Matthias Boehm <mboe...@googlemail.com> > > > wrote: > > > > > >> to summarize, this was an issue of selecting serialized > representations > > >> for large ultra-sparse matrices. Thanks again for sharing your > feedback > > >> with us. > > >> > > >> 1) In-memory representation: In CSR every non-zero will require 12 > bytes > > >> - this is 240MB in your case. The overall memory consumption, however, > > >> depends on the distribution of non-zeros: In CSR, each block with at > > >> least one non-zero requires 4KB for row pointers. Assuming uniform > > >> distribution (the worst case), this gives us 80GB. This is likely the > > >> problem here. Every empty block would have an overhead of 44Bytes but > > >> for the worst-case assumption, there are no empty blocks left. We do > not > > >> use COO for checkpoints because it would slow down subsequent > > operations. > > >> > > >> 2) Serialized/on-disk representation: For sparse datasets that are > > >> expected to exceed aggregate memory, we used to use a serialized > > >> representation (with storage level MEM_AND_DISK_SER) which uses > sparse, > > >> ultra-sparse, or empty representations. In this form, ultra-sparse > > >> blocks require 9 + 16*nnz bytes and empty blocks require 9 bytes. > > >> Therefore, with this representation selected, you're dataset should > > >> easily fit in aggregate memory. Also, note that chkpoint is only a > > >> transformation that persists the rdd, the subsequent operation then > > >> pulls the data into memory. > > >> > > >> At a high-level this was a bug. We missed ultra-sparse representations > > >> when introducing an improvement that stores sparse matrices in MCSR > > >> format in CSR format on checkpoints which eliminated the need to use a > > >> serialized storage level. I just deliver a fix. Now we store such > > >> ultra-sparse matrices again in serialized form which should > > >> significantly reduce the memory pressure. > > >> > > >> Regards, > > >> Matthias > > >> > > >> On 5/3/2017 9:38 AM, Mingyang Wang wrote: > > >> > Hi all, > > >> > > > >> > I was playing with a super sparse matrix FK, 2e7 by 1e6, with only > one > > >> > non-zero value on each row, that is 2e7 non-zero values in total. > > >> > > > >> > With driver memory of 1GB and executor memory of 100GB, I found the > > HOP > > >> > "Spark chkpoint", which is used to pin the FK matrix in memory, is > > >> really > > >> > expensive, as it invokes lots of disk operations. > > >> > > > >> > FK is stored in binary format with 24 blocks, each block is ~45MB, > and > > >> ~1GB > > >> > in total. > > >> > > > >> > For example, with the script as > > >> > > > >> > """ > > >> > FK = read($FK) > > >> > print("Sum of FK = " + sum(FK)) > > >> > """ > > >> > > > >> > things worked fine, and it took ~8s. > > >> > > > >> > While with the script as > > >> > > > >> > """ > > >> > FK = read($FK) > > >> > if (1 == 1) {} > > >> > print("Sum of FK = " + sum(FK)) > > >> > """ > > >> > > > >> > things changed. It took ~92s and I observed lots of disk spills from > > >> logs. > > >> > Based on the stats from Spark UI, it seems the materialized FK > > requires > > >> >> 54GB storage and thus introduces disk operations. > > >> > > > >> > I was wondering, is this the expected behavior of a super sparse > > matrix? > > >> > > > >> > > > >> > Regards, > > >> > Mingyang > > >> > > > >> > > > > > >