# Timeout while writing to CSV **URL:** \ **Category:** Hail Query & hailctl\ **Created:** [March 31, 2020, 2:20am UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354 "2020-03-31T02:20:40Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [March 31, 2020, 2:20am UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/1 "2020-03-31T02:20:40Z")
I’m trying to write a csv: ```auto chip_vars_mt.cols().export('cols.csv', delimiter=',') ``` But I keep getting the following error after a while: ```auto 2020-03-30 17:57:17 Hail: WARN: cols(): Resulting column table is sorted by 'col_key'. To preserve matrix table column order, first unkey columns with 'key_cols_by()' ERROR:root:Exception while sending command. Traceback (most recent call last): File "/home/nicholas/miniconda3/envs/hail/lib/python3.7/site-packages/py4j/java_gateway.py", line 1159, in send_command raise Py4JNetworkError("Answer from Java side is empty") py4j.protocol.Py4JNetworkError: Answer from Java side is empty ``` ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [March 31, 2020, 3:12am UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/2 "2020-03-31T03:12:32Z")
Can you share the log file? The true error should be in there. ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [March 31, 2020, 4:29am UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/3 "2020-03-31T04:29:16Z")
here you go: [hail-20200330-1917-0.2.34-914bd8a10ca2.log](https://discuss.hail.is/uploads/short-url/jjt0YJpQW2Wdo8mf1EXlbcSaMN9.log) (2.4 MB) I don’t see anything wrong immediately. The process takes about 35 min before it craps out. I tried increasing the timeout to 10000s but that didnt seem to help ---
**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\ **Post date:** [March 31, 2020, 1:45pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/4 "2020-03-31T13:45:26Z")
The log appears to just stop about one minute after starting. @tpoterba, maybe you have a better sense? I suspect he’ll want to see the full pipeline to understand what’s happening. ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [March 31, 2020, 2:05pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/5 "2020-03-31T14:05:23Z")
This could be an out-of-memory error. How are you running Hail? Are you running on a cluster or in local mode (laptop, server, etc)? ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [March 31, 2020, 6:03pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/6 "2020-03-31T18:03:33Z")
Running in local mode. I’m using the following config: ```auto [('spark.jars', 'file:///home/nicholas/miniconda3/envs/hail/lib/python3.7/site-packages/hail/hail-all-spark.jar'), ('spark.hadoop.io.compression.codecs', 'org.apache.hadoop.io.compress.DefaultCodec,is.hail.io.compress.BGzipCodec,is.hail.io.compress.BGzipCodecTbi,org.apache.hadoop.io.compress.GzipCodec'), ('spark.ui.showConsoleProgress', 'false'), ('spark.executor.id', 'driver'), ('spark.logConf', 'true'), ('spark.kryo.registrator', 'is.hail.kryo.HailKryoRegistrator'), ('spark.driver.host', 'sci-pvm-nicholas.calicolabs.local'), ('spark.hadoop.mapreduce.input.fileinputformat.split.minsize', '134217728'), ('spark.serializer', 'org.apache.spark.serializer.KryoSerializer'), ('spark.driver.extraClassPath', '/home/nicholas/miniconda3/envs/hail/lib/python3.7/site-packages/hail/hail-all-spark.jar'), ('spark.kryoserializer.buffer.max', '1g'), ('spark.driver.port', '35007'), ('spark.driver.maxResultSize', '0'), ('spark.executor.extraClassPath', './hail-all-spark.jar'), ('spark.master', 'local[*]'), ('spark.repl.local.jars', 'file:///home/nicholas/miniconda3/envs/hail/lib/python3.7/site-packages/hail/hail-all-spark.jar'), ('spark.submit.deployMode', 'client'), ('spark.app.name', 'Hail'), ('spark.driver.memory', '32G'), ('spark.app.id', 'local-1585615971418'), ('spark.executor.heartbeatInterval', '10s'), ('spark.network.timeout', '10000s')] ``` I increased network timeout and driver memory. And I initialize: `hl.init(min_block_size=128)` like so. I was running out of memory previously, so I made these updates per another thread on the forum. I suppose that could be happening again. ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [April 2, 2020, 8:21pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/7 "2020-04-02T20:21:54Z")
In the just-released 0.2.35 we fixed a memory leak present in 0.2.34. Could you try again on this version? ---
**Author:** ![njbernstein](https://avatars.discourse-cdn.com/v4/letter/n/e9bcb4/32.png) [@njbernstein](https://discuss.hail.is/u/njbernstein)\ **Post date:** [April 3, 2020, 5:30pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/8 "2020-04-03T17:30:41Z")
@tpoterba I fixed this yesterday by bumping my memory. I’ll see if things will run with lower memory and the new version. ---
**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\ **Post date:** [April 6, 2020, 3:27pm UTC](https://discuss.hail.is/t/timeout-while-writing-to-csv/1354/9 "2020-04-06T15:27:49Z")
We found a memory leak in 0.2.35 as well as 0.2.34… This should really be fixed in 0.2.36, which we’ll try to release today.