updating SVD code.#1

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hl475 wants to merge 301 commits intomasterfrom

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Commits on Dec 2, 2016

Merge branch 'master' into testSVD

Huamin Li
authored and
Huamin Li
committed

Commits on Dec 3, 2016

[SPARK-18324][ML][DOC] Update ML programming and migration guide for 2.1 release

yanboliang
authored and
jkbradley
committed
[SPARK-18690][PYTHON][SQL] Backward compatibility of unbounded frames

zero323
authored and
rxin
committed
[SPARK-18695] Bump master branch version to 2.2.0-SNAPSHOT
rxin
committed
[SPARK-18362][SQL] Use TextFileFormat in implementation of CSVFileFormat

JoshRosen
authored and
rxin
committed
[SPARK-18586][BUILD] netty-3.8.0.Final.jar has vulnerability CVE-2014-3488 and CVE-2014-0193
srowen
committed
[SPARK-18685][TESTS] Fix URI and release resources after opening in tests at ExecutorClassLoaderSuite

HyukjinKwon
authored and
srowen
committed
[SPARK-18638][BUILD] Upgrade sbt, Zinc, and Maven plugins

weiqingy
authored and
srowen
committed
[SPARK-18582][SQL] Whitelist LogicalPlan operators allowed in correlated subqueries

nsyca
authored and
hvanhovell
committed

Commits on Dec 4, 2016

[SPARK-18081][ML][DOCS] Add user guide for Locality Sensitive Hashing(LSH)

Yunni
authored and
jkbradley
committed
[MINOR][README] Correct Markdown link inside readme

linbojin
authored and
rxin
committed
[SPARK-18091][SQL] Deep if expressions cause Generated SpecificUnsafeProjection code to exceed JVM code size limit

Kapil Singh
authored and
cloud-fan
committed
[SPARK-18661][SQL] Creating a partitioned datasource table should not scan all files for table

ericl
authored and
cloud-fan
committed

Commits on Dec 5, 2016

change the way of genearting random matrix.

Huamin Li
authored and
Huamin Li
committed
[SPARK-18643][SPARKR] SparkR hangs at session start when installed as a package without Spark

felixcheung
authored and
shivaram
committed
[SPARK-18702][SQL] input_file_block_start and input_file_block_length
rxin
committed
[SPARK-18625][ML] OneVsRestModel should support setFeaturesCol and setPredictionCol

zhengruifeng
authored and
yanboliang
committed
[SPARK-18279][DOC][ML][SPARKR] Add R examples to ML programming guide.
yanboliang
committed
[MINOR][DOC] Use SparkR `TRUE` value and add default values for `StructField` in SQL Guide.

dongjoon-hyun
authored and
shivaram
committed
[SPARK-18694][SS] Add StreamingQuery.explain and exception to Python and fix StreamingQueryException

zsxwing
authored and
tdas
committed
[SPARK-18711][SQL] should disable subexpression elimination for LambdaVariable

cloud-fan
authored and
hvanhovell
committed
[DOCS][MINOR] Update location of Spark YARN shuffle jar

nchammas
authored and
Marcelo Vanzin
committed
[SPARK-18719] Add spark.ui.showConsoleProgress to configuration docs

nchammas
authored and
davies
committed

Commits on Dec 6, 2016

[SPARK-18634][PYSPARK][SQL] Corruption and Correctness issues with exploding Python UDFs

viirya
authored and
hvanhovell
committed
[SPARK-18729][SS] Move DataFrame.collect out of synchronized block in MemorySink

zsxwing
authored and
tdas
committed
[SPARK-18657][SPARK-18668] Make StreamingQuery.id persists across restart and not auto-generate StreamingQuery.name
tdas
committed
[SPARK-18720][SQL][MINOR] Code Refactoring of withColumn

gatorsmile
authored and
cloud-fan
committed
[SPARK-18555][SQL] DataFrameNaFunctions.fill miss up original values in long integers

root
authored and
rxin
committed
[SPARK-18722][SS] Move no data rate limit from StreamExecution to ProgressReporter

zsxwing
authored and
tdas
committed
[SPARK-18572][SQL] Add a method `listPartitionNames` to `ExternalCatalog`

Michael Allman
authored and
cloud-fan
committed
[SPARK-18672][CORE] Close recordwriter in SparkHadoopMapReduceWriter before committing

HyukjinKwon
authored and
srowen
committed
[SPARK-18721][SS] Fix ForeachSink with watermark + append

zsxwing
authored and
tdas
committed
[SPARK-18634][SQL][TRIVIAL] Touch-up Generate
hvanhovell
committed
[SPARK-18740] Log spark.app.name in driver logs

peterableda
authored and
Marcelo Vanzin
committed
[SPARK-18714][SQL] Add a simple time function to SparkSession

rxin
authored and
hvanhovell
committed
[SPARK-18671][SS][TEST] Added tests to ensure stability of that all Structured Streaming log formats

tdas
authored and
zsxwing
committed
[SPARK-18374][ML] Incorrect words in StopWords/english.txt

YY-OnCall
authored and
srowen
committed
[SPARK-18744][CORE] Remove workaround for Netty memory leak
zsxwing
committed
[SPARK-18652][PYTHON] Include the example data and third-party licenses in pyspark package.

lins05
authored and
srowen
committed
[SPARK-18697][BUILD] Upgrade sbt plugins

weiqingy
authored and
srowen
committed
[SPARK-18171][MESOS] Show correct framework address in mesos master web ui when the advertised address is used

lins05
authored and
srowen
committed

Commits on Dec 7, 2016

[SPARK-18662] Move resource managers to separate directory

foxish
authored and
Marcelo Vanzin
committed
Revert "[SPARK-18697][BUILD] Upgrade sbt plugins"
srowen
committed
[SPARK-18734][SS] Represent timestamp in StreamingQueryProgress as formatted string instead of millis

tdas
authored and
zsxwing
committed
Update Spark documentation to provide information on how to create External Table

c-sahuja
authored and
rxin
committed
Closes stale & invalid pull requests.
rxin
committed
[SPARK-18671][SS][TEST-MAVEN] Follow up PR to fix test for Maven
tdas
committed
change the way of generating the random matrix and store the transpose explicitly.

Huamin Li
authored and
Huamin Li
committed
[SPARK-18686][SPARKR][ML] Several cleanup and improvements for spark.logit.
yanboliang
committed
[SPARK-18701][ML] Fix Poisson GLM failure due to wrong initialization

actuaryzhang
authored and
srowen
committed
[SPARK-18678][ML] Skewed reservoir sampling in SamplingUtils
srowen
committed
[SPARK-18208][SHUFFLE] Executor OOM due to a growing LongArray in BytesToBytesMap

Jie Xiong
authored and
hvanhovell
committed
[SPARK-17760][SQL] AnalysisException with dataframe pivot when groupBy column is not attribute

aray
authored and
hvanhovell
committed
[SPARK-18764][CORE] Add a warning log when skipping a corrupted file
zsxwing
committed
[SPARK-18762][WEBUI] Web UI should be http:4040 instead of https:4040

sarutak
authored and
Marcelo Vanzin
committed
modify spectralNormEst for generating random vector and normalizing the vector.

Huamin Li
authored and
Huamin Li
committed
[SPARK-18588][TESTS] Fix flaky test: KafkaSourceStressForDontFailOnDataLossSuite

zsxwing
authored and
tdas
committed
[SPARK-18754][SS] Rename recentProgresses to recentProgress

marmbrus
authored and
tdas
committed

Commits on Dec 8, 2016

[SPARK-18654][SQL] Remove unreachable patterns in makeRootConverter

Nathan Howell
authored and
rxin
committed
[SPARK-18633][ML][EXAMPLE] Add multiclass logistic regression summary python example and document

wangmiao1981
authored and
jkbradley
committed
[SPARK-18758][SS] StreamingQueryListener events from a StreamingQuery should be sent only to the listeners in the same session as the query
tdas
committed
[SPARK-18705][ML][DOC] Update user guide to reflect one pass solver for L1 and elastic-net

sethah
authored and
yanboliang
committed
[SPARK-18326][SPARKR][ML] Review SparkR ML wrappers API for 2.1
yanboliang
committed
Close stale pull requests.
rxin
committed
[SPARK-18774][CORE][SQL] Ignore non-existing files when ignoreCorruptFiles is enabled

zsxwing
authored and
rxin
committed
[SPARK-18325][SPARKR][ML] SparkR ML wrappers example code and user guide
yanboliang
committed
[SPARK-18718][TESTS] Skip some test failures due to path length limitation and fix tests to pass on Windows

HyukjinKwon
authored and
srowen
committed
[SPARK-18667][PYSPARK][SQL] Change the way to group row in BatchEvalPythonExec so input_file_name function can work with UDF in pyspark

viirya
authored and
cloud-fan
committed
[SPARK-18662][HOTFIX] Add new resource-managers directories to SparkLauncher.
Marcelo Vanzin
committed
[SPARK-8617][WEBUI] HistoryServer: Include in-progress files during cleanup

seyfe
authored and
Marcelo Vanzin
committed
[SPARK-16589] [PYTHON] Chained cartesian produces incorrect number of records

aray
authored and
davies
committed
[SPARK-18590][SPARKR] build R source package when making distribution

felixcheung
authored and
shivaram
committed
[SPARK-18751][CORE] Fix deadlock when SparkContext.stop is called in Utils.tryOrStopSparkContext
zsxwing
committed
Use different seed for generating random matrix and vectors in partialSVD, spectralNormEst, and tallSkinnySVD.

Huamin Li
authored and
Huamin Li
committed
[SPARK-18760][SQL] Consistent format specification for FileFormats
rxin
committed
Close stale PRs.
rxin
committed
[SPARK-18590][SPARKR] Change the R source build to Hadoop 2.6
shivaram
committed
Set different seed with different partition.

Huamin Li
authored and
Huamin Li
committed
seed to Long.

Huamin Li
authored and
Huamin Li
committed

Commits on Dec 9, 2016

[SPARK-18776][SS] Make Offset for FileStreamSource corrected formatted in json
tdas
committed
[SPARKR][PYSPARK] Fix R source package name to match Spark version. Remove pip tar.gz from distribution
shivaram
committed
[SPARK-18349][SPARKR] Update R API documentation on ml model summary

wangmiao1981
authored and
Felix Cheung
committed
[SPARK-18697][BUILD] Upgrade sbt plugins

weiqingy
authored and
srowen
committed
Copy the SparkR source package with LFTP
shivaram
committed
refactor the code - parallelization.

Huamin Li
authored and
Huamin Li
committed
Copy pyspark and SparkR packages to latest release dir too

felixcheung
authored and
shivaram
committed
[SPARK-18637][SQL] Stateful UDF should be considered as nondeterministic

Zhan Zhang
authored and
cloud-fan
committed
[MINOR][CORE][SQL][DOCS] Typo fixes

jaceklaskowski
authored and
srowen
committed
[SPARK-17822][R] Make JVMObjectTracker a member variable of RBackend
mengxr
committed
[MINOR][SPARKR] Fix SparkR regex in copy command
shivaram
committed
[SPARK-18620][STREAMING][KINESIS] Flatten input rates in timeline for streaming + kinesis

maropu
authored and
srowen
committed
[SPARK-18745][SQL] Fix signed integer overflow due to toInt cast

kiszk
authored and
hvanhovell
committed
[SPARK-4105] retry the fetch or stage if shuffle block is corrupt

Davies Liu
authored and
zsxwing
committed

Commits on Dec 10, 2016

Commits on Dec 11, 2016

[SPARK-18815][SQL] Fix NPE when collecting column stats for string/binary column having only null values

wangzhenhua
authored and
rxin
committed
[SQL][MINOR] simplify a test to fix the maven tests

cloud-fan
authored and
srowen
committed
[SPARK-18809] KCL version to 1.6.2 on master

boneill42
authored and
srowen
committed
[SPARK-18628][ML] Update Scala param and Python param to have quotes

krishnakalyan3
authored and
srowen
committed

Commits on Dec 12, 2016

[SPARK-18790][SS] Keep a general offset history of stream batches

Tyson Condie
authored and
zsxwing
committed
[DOCS][MINOR] Clarify Where AccumulatorV2s are Displayed

Bill Chambers
authored and
srowen
committed
[SPARK-15844][CORE] HistoryServer doesn't come up if spark.authenticate = true

steveloughran
authored and
Marcelo Vanzin
committed
[SPARK-16297][SQL] Fix mapping Microsoft SQLServer dialect

meknio
authored and
Marcelo Vanzin
committed
[SPARK-18752][HIVE] isSrcLocal" value should be set from user query.

Marcelo Vanzin
authored and
gatorsmile
committed
[SPARK-18681][SQL] Fix filtering to compatible with partition keys of type int

wangyum
authored and
hvanhovell
committed
[SPARK-18810][SPARKR] SparkR install.spark does not work for RCs, snapshots

felixcheung
authored and
shivaram
committed

Commits on Dec 13, 2016

[SPARK-18773][CORE] Make commons-crypto config translation consistent.

Marcelo Vanzin
authored and
zsxwing
committed
[SPARK-18796][SS] StreamingQueryManager should not block when starting a query

zsxwing
authored and
tdas
committed
[SPARK-18797][SPARKR] Update spark.logit in sparkr-vignettes

wangmiao1981
authored and
mengxr
committed
[SPARK-18717][SQL] Make code generation for Scala Map work with immutable.Map also

aray
authored and
cloud-fan
committed
[MINOR][CORE][SQL] Remove explicit RDD and Partition overrides

jaceklaskowski
authored and
srowen
committed
[SPARK-18675][SQL] CTAS for hive serde table should work for all hive versions

cloud-fan
authored and
yhuai
committed
[SPARK-13747][CORE] Fix potential ThreadLocal leaks in RPC when using ForkJoinPool

zsxwing
authored and
yhuai
committed
[SPARK-18835][SQL] Don't expose Guava types in the JavaTypeInference API.
Marcelo Vanzin
committed
[SPARK-17932][SQL][FOLLOWUP] Change statement `SHOW TABLES EXTENDED` to `SHOW TABLE EXTENDED`

jiangxb1987
authored and
hvanhovell
committed
[SPARK-18840][YARN] Avoid throw exception when getting token renewal interval in non HDFS security environment

jerryshao
authored and
Marcelo Vanzin
committed
[SPARK-18715][ML] Fix AIC calculations in Binomial GLM

actuaryzhang
authored and
srowen
committed
[SPARK-18471][MLLIB] In LBFGS, avoid sending huge vectors of 0

Anthony Truchet
authored and
srowen
committed
[SPARK-18816][WEB UI] Executors Logs column only ran visibility check on initial table load

ajbozarth
authored and
srowen
committed
[SPARK-18834][SS] Expose event time stats through StreamingQueryProgress
tdas
committed

Commits on Dec 14, 2016

Commits on Dec 15, 2016

[SPARK-18854][SQL] numberedTreeString and apply(i) inconsistent for subqueries
rxin
committed
[SPARK-18865][SPARKR] SparkR vignettes MLP and LDA updates

wangmiao1981
authored and
Felix Cheung
committed
[SPARK-18703][SQL] Drop Staging Directories and Data Files After each Insertion/CTAS of Hive serde Tables

gatorsmile
authored and
cloud-fan
committed
[SPARK-18856][SQL] non-empty partitioned table should not report zero size

cloud-fan
authored and
rxin
committed
[SPARK-18869][SQL] Add TreeNode.p that returns BaseType
rxin
committed
[SPARK-18875][SPARKR][DOCS] Fix R API doc generation by adding `DESCRIPTION` file

dongjoon-hyun
authored and
shivaram
committed
[SPARK-18849][ML][SPARKR][DOC] vignettes final check update

felixcheung
authored and
shivaram
committed
[SPARK-8425][CORE] Application Level Blacklisting
squito
committed
[SPARK-17910][SQL] Allow users to update the comment of a column

jiangxb1987
authored and
rxin
committed
[SPARK-18870] Disallowed Distinct Aggregations on Streaming Datasets
tdas
committed
[SPARK-18826][SS] Add 'latestFirst' option to FileStreamSource

zsxwing
authored and
tdas
committed
[SPARK-18888] partitionBy in DataStreamWriter in Python throws _to_seq not defined

brkyvz
authored and
tdas
committed
[SPARK-8425][SCHEDULER][HOTFIX] fix scala 2.10 compile error

squito
authored and
rxin
committed
[SPARK-18868][FLAKY-TEST] Deflake StreamingQueryListenerSuite: single listener, check trigger...

brkyvz
authored and
zsxwing
committed

Commits on Dec 16, 2016

[MINOR] Only rename SparkR tar.gz if names mismatch

shivaram
authored and
rxin
committed
[MINOR] Handle fact that mv is different on linux, mac
shivaram
committed
[SPARK-18892][SQL] Alias percentile_approx approx_percentile
rxin
committed
[SPARK-18845][GRAPHX] PageRank has incorrect initialization value that leads to slow convergence

aray
authored and
ankurdave
committed
[SPARK-18850][SS] Make StreamExecution and progress classes serializable

zsxwing
authored and
tdas
committed
[SPARK-18742][CORE] Clarify that user-defined BroadcastFactory is not supported

root
authored and
srowen
committed
[SPARK-18108][SQL] Fix a schema inconsistent bug that makes a parquet reader fail to read data

maropu
authored and
cloud-fan
committed
[SPARK-18723][DOC] Expanded programming guide information on wholeTex…

michalsenkyr
authored and
srowen
committed
[SPARK-18708][CORE] Improvement/improve docs in spark context file

Aliaksandr.Bedrytski
authored and
srowen
committed
[MINOR][BUILD] Fix lint-check failures and javadoc8 break

HyukjinKwon
authored and
srowen
committed
[SPARK-18897][SPARKR] Fix SparkR SQL Test to drop test table

dongjoon-hyun
authored and
shivaram
committed
[SPARK-17769][CORE][SCHEDULER] Some FetchFailure refactoring

markhamstra
authored and
Marcelo Vanzin
committed
[SPARK-18904][SS][TESTS] Merge two FileStreamSourceSuite files
zsxwing
committed

Commits on Dec 17, 2016

[SPARK-18895][TESTS] Fix resource-closing-related and path-related test failures in identified ones on Windows

HyukjinKwon
authored and
shivaram
committed
[SPARK-18485][CORE] Underlying integer overflow when create ChunkedByteBufferOutputStream in MemoryStore

uncleGen
authored and
srowen
committed
[SPARK-18849][ML][SPARKR][DOC] vignettes final check reorg

felixcheung
authored and
Felix Cheung
committed

Commits on Dec 18, 2016

[SPARK-18918][DOC] Missing </td> in Configuration page

gatorsmile
authored and
srowen
committed
[SPARK-18827][CORE] Fix cannot read broadcast on disk

wangyum
authored and
srowen
committed

Commits on Dec 19, 2016

[SPARK-18356][ML] KMeans should cache RDD before training

ZakariaHili
authored and
srowen
committed
[SPARK-18700][SQL] Add StripedLock for each table's relation in cache

xuanyuanking
authored and
hvanhovell
committed
[SPARK-18921][SQL] check database existence with Hive.databaseExists instead of getDatabase

cloud-fan
authored and
yhuai
committed
[SPARK-18624][SQL] Implicit cast ArrayType(InternalType)

jiangxb1987
authored and
hvanhovell
committed
[SPARK-18836][CORE] Serialize one copy of task metrics in DAGScheduler

shivaram
authored and
kayousterhout
committed

Commits on Dec 20, 2016

Commits on Dec 21, 2016

Commits on Dec 22, 2016

[SPARK-17807][CORE] split test-tags into test-JAR

ryan-williams
authored and
Marcelo Vanzin
committed
[SPARK-18234][SS] Made update mode public
tdas
committed
[SPARK-18528][SQL] Fix a bug to initialise an iterator of aggregation buffer

maropu
authored and
hvanhovell
committed
[SPARK-18903][SPARKR] Add API to get SparkUI URL

felixcheung
authored and
Felix Cheung
committed
[FLAKY-TEST] InputStreamsSuite.socket input stream

brkyvz
authored and
tdas
committed
[BUILD] make-distribution should find JAVA_HOME for non-RHEL systems

felixcheung
authored and
Felix Cheung
committed
[SPARK-18908][SS] Creating StreamingQueryException should check if logicalPlan is created
zsxwing
committed
[SQL] Minor readability improvement for partition handling code

rxin
authored and
cloud-fan
committed
[DOC] bucketing is applicable to all file-based data sources
rxin
committed
[SPARK-18953][CORE][WEB UI] Do now show the link to a dead worker on the master page

dongjoon-hyun
authored and
srowen
committed
[SPARK-18922][TESTS] Fix more resource-closing-related and path-related test failures in identified ones on Windows

HyukjinKwon
authored and
srowen
committed
[SPARK-16975][SQL][FOLLOWUP] Do not duplicately check file paths in data sources implementing FileFormat

HyukjinKwon
authored and
rxin
committed
[SPARK-18973][SQL] Remove SortPartitions and RedistributeData

rxin
authored and
hvanhovell
committed
[SPARK-18975][CORE] Add an API to remove SparkListener

jerryshao
authored and
rxin
committed
[SPARK-18537][WEB UI] Add a REST api to serve spark streaming information

saturday_s
authored and
Marcelo Vanzin
committed
refactor spectralNormEst.

Huamin Li
authored and
Huamin Li
committed
initial base.

hl475
authored and
Huamin Li
committed
clean up the code and comments.

hl475
authored and
Huamin Li
committed
clean up the code and comments again.

hl475
authored and
Huamin Li
committed
modify the code to address Mark's comments.

hl475
authored and
Huamin Li
committed
modify the code to address Mark's comments: partialSVD will do orthonormalization twice in the last step; add output of max values of non-diagonal entries of left and right singular values to parti…

hl475
authored and
Huamin Li
committed
modify tallSkinnySVD: do tallSkinnyQR twice instead of once to have pure orthonormalization of final left and right singular vectors.

hl475
authored and
Huamin Li
committed
Add inline comments to RowMatrix.scala

hl475
authored and
Huamin Li
committed
Use tallSkinnySVD for orthonormal in partialSVD; add isGram and ifTwice to tallSkinnySVD.

hl475
authored and
Huamin Li
committed
Add more inline comments to tallSkinnySVD.

hl475
authored and
Huamin Li
committed
Modify the code according to Mark's comment: add parameter ifTwice to unit test; update partialSVD so that ifTwice = false during the subspace iterations, while ifTwice = true during lastStep; chan…

hl475
authored and
Huamin Li
committed
remove code duplication from lastStep; add unit tests of testing parameter ifTwice.

hl475
authored and
Huamin Li
committed
change value of rCond.

hl475
authored and
Huamin Li
committed
Refactoring the code.

hl475
authored and
Huamin Li
committed
add computeSVD to unit tests just for comparison.

hl475
authored and
Huamin Li
committed
refactoring the code.

hl475
authored and
Huamin Li
committed
refactoring the code and add another unit test of different combinations of isGram and ifTwice.

hl475
authored and
Huamin Li
committed
refactoring the code to address Mark's comment.

hl475
authored and
Huamin Li
committed
refactoring the code to pass the code style check.

hl475
authored and
Huamin Li
committed
refactoring the test code and tobreeze/asbreeze

hl475
authored and
Huamin Li
committed
refactoring the unit test and adding comment to toBreeze v.s. asBreeze

hl475
authored and
Huamin Li
committed
add an svd example to spark

hl475
authored and
Huamin Li
committed
add two examples

hl475
authored and
Huamin Li
committed
refactoring the test code and tobreeze/asbreeze

hl475
authored and
Huamin Li
committed
Refactoring the code:

hl475
authored and
Huamin Li
committed
modify the code to address Mark's comments.

hl475
authored and
Huamin Li
committed
modify inline comments in RowMatrix to address Mark's comments.

hl475
authored and
Huamin Li
committed
add shuffle.scala

Huamin Li
authored and
Huamin Li
committed
change the way of genearting random matrix.

Huamin Li
authored and
Huamin Li
committed
change the way of generating the random matrix and store the transpose explicitly.

Huamin Li
authored and
Huamin Li
committed
modify spectralNormEst for generating random vector and normalizing the vector.

Huamin Li
authored and
Huamin Li
committed
Use different seed for generating random matrix and vectors in partialSVD, spectralNormEst, and tallSkinnySVD.

Huamin Li
authored and
Huamin Li
committed
Set different seed with different partition.

Huamin Li
authored and
Huamin Li
committed
seed to Long.

Huamin Li
authored and
Huamin Li
committed
refactor the code - parallelization.

Huamin Li
authored and
Huamin Li
committed
V in partailSVD now is BlockMatrix.

Huamin Li
authored and
Huamin Li
committed
refactor spectralNormEst.

Huamin Li
authored and
Huamin Li
committed
Merge branch 'testSVD' of https://github.com/hl475/svd into testSVD

Huamin Li
authored and
Huamin Li
committed