[DM-9006] git-lfs related lsstsw installation error on macOS Sierra - Jira

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Type: Story
Status: Done
Resolution: Done
Fix Version/s: None
Component/s: Developer Infrastructure, lsst_build, lsstsw
Labels:
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Story Points:
0.375
Team:
SQuaRE

Description

I tried to do my first lsstsw-based installation on a new macOS Sierra computer and got this error during the afwdata build:

             afwdata: Traceback (most recent call last):

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/bin/lsst-build", line 51,in <module>

    args.func(args)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 762, in run

    manifest = p.construct(args.products)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 725, in construct

    self._add_product_tree(products, name)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 713, in _add_product_tree

    dependencies.append(self._add_product_tree(products, dprod.name))

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 713, in _add_product_tree

    dependencies.append(self._add_product_tree(products, dprod.name))

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 713, in _add_product_tree

    dependencies.append(self._add_product_tree(products, dprod.name))

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 713, in _add_product_tree

    dependencies.append(self._add_product_tree(products, dprod.name))

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 696, in _add_product_tree

    ref, sha1 = self.product_fetcher.fetch(product_name)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 333, in fetch

    git.checkout("--force", ref)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/git.py", line 49, in checkout

    return self('checkout', *args, **kwargs)

  File "/Users/jsick/lsst/qa-system/lsstsw/lsst_build/python/lsst/ci/git.py", line 44, in __call__

    raise GitError(retcode, cmd, stdout, stderr)

lsst.ci.git.GitError: Command '['git', 'checkout', '--force', 'master']' returned non-zero exit status 128.

stdout:

stderr:

Error: unknown command "filter-process" for "git-lfs"

Run 'git-lfs --help' for usage.

fatal: The remote end hung up unexpectedly

Details:

This is a Python 3 lsstsw installation but I also replicated the same issue with a Python 2.7 lsstsw.
The git-lfs version I see in lsstsw is git-lfs/1.2.0 (GitHub; darwin amd64; go 1.6.1; git 9bd3b8e).
My computer also has a git-lfs 1.5.4 from Homebrew and I've been able to successfully clone afwdata with this git-lfs (no configuration issues).
I've also manually cloned afwdata using the lsstsw-provided git-lfs 1.2.0 (no problem with that git-lfs in my environment).

This leads me to think that there's some issue with how git/git-lfs is being controlled by lsst_build on macOS Sierra.

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Joshua Hoblitt added a comment - 25/Jan/17 5:43 PM

I believe I've reproduced this on Sierra. My current hunch is that git lfs OSX build is broken on Sierra.

mac-os-sierra-build-3:lsstsw square$ rebuild afwdata

             afwdata: Traceback (most recent call last):

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/bin/lsst-build", line 51, in <module>

    args.func(args)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 762, in run

    manifest = p.construct(args.products)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 725, in construct

    self._add_product_tree(products, name)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 696, in _add_product_tree

    ref, sha1 = self.product_fetcher.fetch(product_name)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 311, in fetch

    raise Exception("Failed to clone product '%s' from any of the offered repositories" % product)

Exception: Failed to clone product 'afwdata' from any of the offered repositories

mac-os-sierra-build-3:lsstsw square$

mac-os-sierra-build-3:lsstsw square$ rebuild afwdata

             afwdata:

Traceback (most recent call last):

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/bin/lsst-build", line 51, in <module>

    args.func(args)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 762, in run

    manifest = p.construct(args.products)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 725, in construct

    self._add_product_tree(products, name)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 696, in _add_product_tree

    ref, sha1 = self.product_fetcher.fetch(product_name)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py", line 333, in fetch

    git.checkout("--force", ref)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/git.py", line 49, in checkout

    return self('checkout', *args, **kwargs)

  File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/git.py", line 44, in __call__

    raise GitError(retcode, cmd, stdout, stderr)

lsst.ci.git.GitError: Command '['git', 'checkout', '--force', 'master']' returned non-zero exit status 128.

stdout:

stderr:

Downloading CFHT/D4/cal-53535-i-797722_5.fits (93.60 MB)

Downloading CFHT/D4/cal-53535-i-797722_5_tmpl.fits (84.34 MB)

Downloading CFHT/D4/cal-53535-i-797722_6.fits (93.60 MB)

Downloading CFHT/D4/cal-53535-i-797722_6_tmpl.fits (84.34 MB)

Downloading CFHT/D4/cal-53535-i-797722_7.fits (93.60 MB)

Downloading CFHT/D4/cal-53535-i-797722_7_tmpl.fits (84.34 MB)

Downloading CFHT/D4/cal-53535-i-797722_8.fits (93.60 MB)

Downloading CFHT/D4/cal-53535-i-797722_8_tmpl.fits (84.34 MB)

Downloading CFHT/D4/cal-53535-i-797722_9.fits (93.60 MB)

failed MSpanList_Insert 0xc143b0 0x270fd0d540d2d 0x0 0x0

fatal error: MSpanList_Insert

runtime stack:

runtime.throw(0x5f1530, 0x10)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/panic.go:530 +0x90

runtime.(*mSpanList).insert(0x8503a8, 0xc143b0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:933 +0x293

runtime.(*mheap).freeSpanLocked(0x84fba0, 0xc143b0, 0x100, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:809 +0x4be

runtime.(*mheap).grow(0x84fba0, 0x80, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:675 +0x2a0

runtime.(*mheap).allocSpanLocked(0x84fba0, 0x80, 0xc81ffd8100)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:553 +0x4e3

runtime.(*mheap).alloc_m(0x84fba0, 0x80, 0x100000000, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:437 +0x119

runtime.(*mheap).alloc.func1()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:502 +0x41

runtime.systemstack(0x700001a43dc8)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:307 +0xab

runtime.(*mheap).alloc(0x84fba0, 0x80, 0x10100000000, 0xc82001ea00)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/mheap.go:503 +0x63

runtime.largeAlloc(0x100000, 0x1, 0xda2cb0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/malloc.go:766 +0xb3

runtime.mallocgc.func3()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/malloc.go:664 +0x33

runtime.systemstack(0xc820020000)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:291 +0x79

runtime.mstart()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/proc.go:1048

goroutine 1 [running]:

runtime.systemstack_switch()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:245 fp=0xc820193188 sp=0xc820193180

runtime.mallocgc(0x100000, 0x42ab00, 0x1, 0x5)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/malloc.go:665 +0x9eb fp=0xc820193260 sp=0xc820193188

runtime.newarray(0x42ab00, 0x100000, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/malloc.go:798 +0xc9 fp=0xc8201932a0 sp=0xc820193260

runtime.makeslice(0x419140, 0x100000, 0x100000, 0x0, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/slice.go:32 +0x165 fp=0xc8201932f0 sp=0xc8201932a0

github.com/github/git-lfs/lfs.Stack(0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go:565 +0x4a fp=0xc820193340 sp=0xc8201932f0

github.com/github/git-lfs/lfs.newWrappedError(0xda2c60, 0xc8203e55f0, 0xc820116540, 0x1c0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go:313 +0x1a3 fp=0xc820193430 sp=0xc820193340

github.com/github/git-lfs/lfs.Errorf(0xda2c60, 0xc8203e55f0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go:231 +0x175 fp=0xc8201934c8 sp=0xc820193430

github.com/github/git-lfs/lfs.Error(0xda2c60, 0xc8203e55f0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go:217 +0x54 fp=0xc820193518 sp=0xc8201934c8

github.com/github/git-lfs/lfs.doHttpRequest(0xc8203922a0, 0xc8203e4960, 0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/client.go:510 +0x50d fp=0xc820193638 sp=0xc820193518

github.com/github/git-lfs/lfs.doStorageRequest(0xc8203922a0, 0x5acb00, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/client.go:470 +0x7b fp=0xc820193678 sp=0xc820193638

github.com/github/git-lfs/lfs.DownloadLegacy(0xc8200a482a, 0x40, 0x0, 0x0, 0x83e5b0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/client.go:159 +0x1f4 fp=0xc8201936e0 sp=0xc820193678

github.com/github/git-lfs/lfs.Download(0xc8200a482a, 0x40, 0x5d9a800, 0x0, 0x0, 0x2, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/client.go:118 +0x7b fp=0xc8201937d8 sp=0xc8201936e0

github.com/github/git-lfs/lfs.downloadFile(0xc04308, 0xc82008a008, 0xc82008f3b0, 0x7fff5fbff1df, 0x21, 0xc8200a47e0, 0x8a, 0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/pointer_smudge.go:125 +0x267 fp=0xc820193938 sp=0xc8201937d8

github.com/github/git-lfs/lfs.PointerSmudge(0xc04308, 0xc82008a008, 0xc82008f3b0, 0x7fff5fbff1df, 0x21, 0x1, 0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/pointer_smudge.go:58 +0x31c fp=0xc820193a30 sp=0xc820193938

github.com/github/git-lfs/lfs.(*Pointer).Smudge(0xc82008f3b0, 0xc04308, 0xc82008a008, 0x7fff5fbff1df, 0x21, 0x1, 0x0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/lfs/pointer.go:61 +0x75 fp=0xc820193a80 sp=0xc820193a30

github.com/github/git-lfs/commands.smudgeCommand(0x8467a0, 0xc820077930, 0x1, 0x1)

	/Users/rick/go/src/github.com/github/git-lfs/commands/command_smudge.go:70 +0xb81 fp=0xc820193ce0 sp=0xc820193a80

github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra.(*Command).execute(0x8467a0, 0xc820077880, 0x1, 0x1, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra/command.go:477 +0x3f4 fp=0xc820193da8 sp=0xc820193ce0

github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra.(*Command).Execute(0x8477e0, 0x0, 0x0)

	/Users/rick/go/src/github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra/command.go:551 +0x46a fp=0xc820193eb0 sp=0xc820193da8

github.com/github/git-lfs/commands.Run()

	/Users/rick/go/src/github.com/github/git-lfs/commands/commands.go:99 +0x23 fp=0xc820193ed0 sp=0xc820193eb0

main.main()

	/Users/rick/go/src/github.com/github/git-lfs/git-lfs.go:34 +0x12e fp=0xc820193f40 sp=0xc820193ed0

runtime.main()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/proc.go:188 +0x2b0 fp=0xc820193f90 sp=0xc820193f40

runtime.goexit()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:1998 +0x1 fp=0xc820193f98 sp=0xc820193f90

goroutine 17 [syscall, locked to thread]:

runtime.goexit()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:1998 +0x1

goroutine 20 [syscall]:

os/signal.signal_recv(0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/sigqueue.go:116 +0x132

os/signal.loop()

	/usr/local/Cellar/go/1.6.1/libexec/src/os/signal/signal_unix.go:22 +0x18

created by os/signal.init.1

	/usr/local/Cellar/go/1.6.1/libexec/src/os/signal/signal_unix.go:28 +0x37

goroutine 23 [select, locked to thread]:

runtime.gopark(0x68ab80, 0xc82002af28, 0x5a0de8, 0x6, 0x18, 0x2)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/proc.go:262 +0x163

runtime.selectgoImpl(0xc82002af28, 0x0, 0x18)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/select.go:392 +0xa67

runtime.selectgo(0xc82002af28)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/select.go:215 +0x12

runtime.ensureSigM.func1()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/signal1_unix.go:279 +0x32c

runtime.goexit()

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/asm_amd64.s:1998 +0x1

goroutine 24 [chan receive]:

main.main.func1(0xc820074fc0, 0xc820077820)

	/Users/rick/go/src/github.com/github/git-lfs/git-lfs.go:22 +0x66

created by main.main

	/Users/rick/go/src/github.com/github/git-lfs/git-lfs.go:32 +0x129

goroutine 4 [select]:

net/http.(*persistConn).writeLoop(0xc820137860)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/http/transport.go:1273 +0x472

created by net/http.(*Transport).dialConn

	/usr/local/Cellar/go/1.6.1/libexec/src/net/http/transport.go:854 +0x10cb

goroutine 3 [IO wait]:

net.runtime_pollWait(0xc09b28, 0x72, 0xc8201a6000)

	/usr/local/Cellar/go/1.6.1/libexec/src/runtime/netpoll.go:160 +0x60

net.(*pollDesc).Wait(0xc820139330, 0x72, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/fd_poll_runtime.go:73 +0x3a

net.(*pollDesc).WaitRead(0xc820139330, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/fd_poll_runtime.go:78 +0x36

net.(*netFD).Read(0xc8201392d0, 0xc8201a6000, 0x1000, 0x1000, 0x0, 0xc00028, 0xc8200760a0)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/fd_unix.go:250 +0x23a

net.(*conn).Read(0xc82008a288, 0xc8201a6000, 0x1000, 0x1000, 0x0, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/net.go:172 +0xe4

crypto/tls.(*block).readFromUntil(0xc8201338f0, 0xc09c38, 0xc82008a288, 0x5, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/crypto/tls/conn.go:460 +0xcc

crypto/tls.(*Conn).readRecord(0xc8201a4000, 0x68ac17, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/crypto/tls/conn.go:562 +0x2d1

crypto/tls.(*Conn).Read(0xc8201a4000, 0xc8201a7000, 0x1000, 0x1000, 0x0, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/crypto/tls/conn.go:939 +0x167

net/http.noteEOFReader.Read(0x98c318, 0xc8201a4000, 0xc8201378c8, 0xc8201a7000, 0x1000, 0x1000, 0x6703, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/http/transport.go:1683 +0x67

net/http.(*noteEOFReader).Read(0xc820448560, 0xc8201a7000, 0x1000, 0x1000, 0xc82004dd0d, 0x0, 0x0)

	<autogenerated>:284 +0xd0

bufio.(*Reader).fill(0xc8202f4840)

	/usr/local/Cellar/go/1.6.1/libexec/src/bufio/bufio.go:97 +0x1e9

bufio.(*Reader).Peek(0xc8202f4840, 0x1, 0x0, 0x0, 0x0, 0x0, 0x0)

	/usr/local/Cellar/go/1.6.1/libexec/src/bufio/bufio.go:132 +0xcc

net/http.(*persistConn).readLoop(0xc820137860)

	/usr/local/Cellar/go/1.6.1/libexec/src/net/http/transport.go:1069 +0x177

created by net/http.(*Transport).dialConn

	/usr/local/Cellar/go/1.6.1/libexec/src/net/http/transport.go:853 +0x10a6

error: external filter git-lfs smudge %f failed 2

error: external filter git-lfs smudge %f failed

fatal: CFHT/D4/cal-53535-i-797722_9.fits: smudge filter lfs failed

Show

Joshua Hoblitt added a comment - 25/Jan/17 5:43 PM I believe I've reproduced this on Sierra. My current hunch is that git lfs OSX build is broken on Sierra. mac-os-sierra-build- 3 :lsstsw square$ rebuild afwdata afwdata: Traceback (most recent call last): File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/bin/lsst-build" , line 51 , in <module> args.func(args) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 762 , in run manifest = p.construct(args.products) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 725 , in construct self._add_product_tree(products, name) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 696 , in _add_product_tree ref, sha1 = self.product_fetcher.fetch(product_name) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 311 , in fetch raise Exception( "Failed to clone product '%s' from any of the offered repositories" % product) Exception: Failed to clone product 'afwdata' from any of the offered repositories mac-os-sierra-build- 3 :lsstsw square$ mac-os-sierra-build- 3 :lsstsw square$ rebuild afwdata afwdata: Traceback (most recent call last): File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/bin/lsst-build" , line 51 , in <module> args.func(args) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 762 , in run manifest = p.construct(args.products) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 725 , in construct self._add_product_tree(products, name) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 696 , in _add_product_tree ref, sha1 = self.product_fetcher.fetch(product_name) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/prepare.py" , line 333 , in fetch git.checkout( "--force" , ref) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/git.py" , line 49 , in checkout return self( 'checkout' , *args, **kwargs) File "/Users/square/jhoblitt-lsstsw/lsstsw/lsst_build/python/lsst/ci/git.py" , line 44 , in __call__ raise GitError(retcode, cmd, stdout, stderr) lsst.ci.git.GitError: Command '[' git ', ' checkout ', ' --force ', ' master ']' returned non-zero exit status 128 . stdout: stderr: Downloading CFHT/D4/cal- 53535 -i-797722_5.fits ( 93.60 MB) Downloading CFHT/D4/cal- 53535 -i-797722_5_tmpl.fits ( 84.34 MB) Downloading CFHT/D4/cal- 53535 -i-797722_6.fits ( 93.60 MB) Downloading CFHT/D4/cal- 53535 -i-797722_6_tmpl.fits ( 84.34 MB) Downloading CFHT/D4/cal- 53535 -i-797722_7.fits ( 93.60 MB) Downloading CFHT/D4/cal- 53535 -i-797722_7_tmpl.fits ( 84.34 MB) Downloading CFHT/D4/cal- 53535 -i-797722_8.fits ( 93.60 MB) Downloading CFHT/D4/cal- 53535 -i-797722_8_tmpl.fits ( 84.34 MB) Downloading CFHT/D4/cal- 53535 -i-797722_9.fits ( 93.60 MB) failed MSpanList_Insert 0xc143b0 0x270fd0d540d2d 0x0 0x0 fatal error: MSpanList_Insert runtime stack: runtime. throw ( 0x5f1530 , 0x10 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/panic.go: 530 + 0x90 runtime.(*mSpanList).insert( 0x8503a8 , 0xc143b0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 933 + 0x293 runtime.(*mheap).freeSpanLocked( 0x84fba0 , 0xc143b0 , 0x100 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 809 + 0x4be runtime.(*mheap).grow( 0x84fba0 , 0x80 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 675 + 0x2a0 runtime.(*mheap).allocSpanLocked( 0x84fba0 , 0x80 , 0xc81ffd8100 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 553 + 0x4e3 runtime.(*mheap).alloc_m( 0x84fba0 , 0x80 , 0x100000000 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 437 + 0x119 runtime.(*mheap).alloc.func1() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 502 + 0x41 runtime.systemstack( 0x700001a43dc8 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 307 + 0xab runtime.(*mheap).alloc( 0x84fba0 , 0x80 , 0x10100000000 , 0xc82001ea00 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/mheap.go: 503 + 0x63 runtime.largeAlloc( 0x100000 , 0x1 , 0xda2cb0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/malloc.go: 766 + 0xb3 runtime.mallocgc.func3() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/malloc.go: 664 + 0x33 runtime.systemstack( 0xc820020000 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 291 + 0x79 runtime.mstart() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/proc.go: 1048 goroutine 1 [running]: runtime.systemstack_switch() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 245 fp= 0xc820193188 sp= 0xc820193180 runtime.mallocgc( 0x100000 , 0x42ab00 , 0x1 , 0x5 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/malloc.go: 665 + 0x9eb fp= 0xc820193260 sp= 0xc820193188 runtime.newarray( 0x42ab00 , 0x100000 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/malloc.go: 798 + 0xc9 fp= 0xc8201932a0 sp= 0xc820193260 runtime.makeslice( 0x419140 , 0x100000 , 0x100000 , 0x0 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/slice.go: 32 + 0x165 fp= 0xc8201932f0 sp= 0xc8201932a0 github.com/github/git-lfs/lfs.Stack( 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go: 565 + 0x4a fp= 0xc820193340 sp= 0xc8201932f0 github.com/github/git-lfs/lfs.newWrappedError( 0xda2c60 , 0xc8203e55f0 , 0xc820116540 , 0x1c0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go: 313 + 0x1a3 fp= 0xc820193430 sp= 0xc820193340 github.com/github/git-lfs/lfs.Errorf( 0xda2c60 , 0xc8203e55f0 , 0x0 , 0x0 , 0x0 , 0x0 , 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go: 231 + 0x175 fp= 0xc8201934c8 sp= 0xc820193430 github.com/github/git-lfs/lfs.Error( 0xda2c60 , 0xc8203e55f0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/errors.go: 217 + 0x54 fp= 0xc820193518 sp= 0xc8201934c8 github.com/github/git-lfs/lfs.doHttpRequest( 0xc8203922a0 , 0xc8203e4960 , 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/client.go: 510 + 0x50d fp= 0xc820193638 sp= 0xc820193518 github.com/github/git-lfs/lfs.doStorageRequest( 0xc8203922a0 , 0x5acb00 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/client.go: 470 + 0x7b fp= 0xc820193678 sp= 0xc820193638 github.com/github/git-lfs/lfs.DownloadLegacy( 0xc8200a482a , 0x40 , 0x0 , 0x0 , 0x83e5b0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/client.go: 159 + 0x1f4 fp= 0xc8201936e0 sp= 0xc820193678 github.com/github/git-lfs/lfs.Download( 0xc8200a482a , 0x40 , 0x5d9a800 , 0x0 , 0x0 , 0x2 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/client.go: 118 + 0x7b fp= 0xc8201937d8 sp= 0xc8201936e0 github.com/github/git-lfs/lfs.downloadFile( 0xc04308 , 0xc82008a008 , 0xc82008f3b0 , 0x7fff5fbff1df , 0x21 , 0xc8200a47e0 , 0x8a , 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/pointer_smudge.go: 125 + 0x267 fp= 0xc820193938 sp= 0xc8201937d8 github.com/github/git-lfs/lfs.PointerSmudge( 0xc04308 , 0xc82008a008 , 0xc82008f3b0 , 0x7fff5fbff1df , 0x21 , 0x1 , 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/pointer_smudge.go: 58 + 0x31c fp= 0xc820193a30 sp= 0xc820193938 github.com/github/git-lfs/lfs.(*Pointer).Smudge( 0xc82008f3b0 , 0xc04308 , 0xc82008a008 , 0x7fff5fbff1df , 0x21 , 0x1 , 0x0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/lfs/pointer.go: 61 + 0x75 fp= 0xc820193a80 sp= 0xc820193a30 github.com/github/git-lfs/commands.smudgeCommand( 0x8467a0 , 0xc820077930 , 0x1 , 0x1 ) /Users/rick/go/src/github.com/github/git-lfs/commands/command_smudge.go: 70 + 0xb81 fp= 0xc820193ce0 sp= 0xc820193a80 github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra.(*Command).execute( 0x8467a0 , 0xc820077880 , 0x1 , 0x1 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra/command.go: 477 + 0x3f4 fp= 0xc820193da8 sp= 0xc820193ce0 github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra.(*Command).Execute( 0x8477e0 , 0x0 , 0x0 ) /Users/rick/go/src/github.com/github/git-lfs/vendor/_nuts/github.com/spf13/cobra/command.go: 551 + 0x46a fp= 0xc820193eb0 sp= 0xc820193da8 github.com/github/git-lfs/commands.Run() /Users/rick/go/src/github.com/github/git-lfs/commands/commands.go: 99 + 0x23 fp= 0xc820193ed0 sp= 0xc820193eb0 main.main() /Users/rick/go/src/github.com/github/git-lfs/git-lfs.go: 34 + 0x12e fp= 0xc820193f40 sp= 0xc820193ed0 runtime.main() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/proc.go: 188 + 0x2b0 fp= 0xc820193f90 sp= 0xc820193f40 runtime.goexit() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 1998 + 0x1 fp= 0xc820193f98 sp= 0xc820193f90 goroutine 17 [syscall, locked to thread]: runtime.goexit() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 1998 + 0x1 goroutine 20 [syscall]: os/signal.signal_recv( 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/sigqueue.go: 116 + 0x132 os/signal.loop() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/os/signal/signal_unix.go: 22 + 0x18 created by os/signal.init. 1 /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/os/signal/signal_unix.go: 28 + 0x37 goroutine 23 [select, locked to thread]: runtime.gopark( 0x68ab80 , 0xc82002af28 , 0x5a0de8 , 0x6 , 0x18 , 0x2 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/proc.go: 262 + 0x163 runtime.selectgoImpl( 0xc82002af28 , 0x0 , 0x18 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/select.go: 392 + 0xa67 runtime.selectgo( 0xc82002af28 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/select.go: 215 + 0x12 runtime.ensureSigM.func1() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/signal1_unix.go: 279 + 0x32c runtime.goexit() /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/asm_amd64.s: 1998 + 0x1 goroutine 24 [chan receive]: main.main.func1( 0xc820074fc0 , 0xc820077820 ) /Users/rick/go/src/github.com/github/git-lfs/git-lfs.go: 22 + 0x66 created by main.main /Users/rick/go/src/github.com/github/git-lfs/git-lfs.go: 32 + 0x129 goroutine 4 [select]: net/http.(*persistConn).writeLoop( 0xc820137860 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/http/transport.go: 1273 + 0x472 created by net/http.(*Transport).dialConn /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/http/transport.go: 854 + 0x10cb goroutine 3 [IO wait]: net.runtime_pollWait( 0xc09b28 , 0x72 , 0xc8201a6000 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/runtime/netpoll.go: 160 + 0x60 net.(*pollDesc).Wait( 0xc820139330 , 0x72 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/fd_poll_runtime.go: 73 + 0x3a net.(*pollDesc).WaitRead( 0xc820139330 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/fd_poll_runtime.go: 78 + 0x36 net.(*netFD).Read( 0xc8201392d0 , 0xc8201a6000 , 0x1000 , 0x1000 , 0x0 , 0xc00028 , 0xc8200760a0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/fd_unix.go: 250 + 0x23a net.(*conn).Read( 0xc82008a288 , 0xc8201a6000 , 0x1000 , 0x1000 , 0x0 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/net.go: 172 + 0xe4 crypto/tls.(*block).readFromUntil( 0xc8201338f0 , 0xc09c38 , 0xc82008a288 , 0x5 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/crypto/tls/conn.go: 460 + 0xcc crypto/tls.(*Conn).readRecord( 0xc8201a4000 , 0x68ac17 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/crypto/tls/conn.go: 562 + 0x2d1 crypto/tls.(*Conn).Read( 0xc8201a4000 , 0xc8201a7000 , 0x1000 , 0x1000 , 0x0 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/crypto/tls/conn.go: 939 + 0x167 net/http.noteEOFReader.Read( 0x98c318 , 0xc8201a4000 , 0xc8201378c8 , 0xc8201a7000 , 0x1000 , 0x1000 , 0x6703 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/http/transport.go: 1683 + 0x67 net/http.(*noteEOFReader).Read( 0xc820448560 , 0xc8201a7000 , 0x1000 , 0x1000 , 0xc82004dd0d , 0x0 , 0x0 ) <autogenerated>: 284 + 0xd0 bufio.(*Reader).fill( 0xc8202f4840 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/bufio/bufio.go: 97 + 0x1e9 bufio.(*Reader).Peek( 0xc8202f4840 , 0x1 , 0x0 , 0x0 , 0x0 , 0x0 , 0x0 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/bufio/bufio.go: 132 + 0xcc net/http.(*persistConn).readLoop( 0xc820137860 ) /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/http/transport.go: 1069 + 0x177 created by net/http.(*Transport).dialConn /usr/local/Cellar/go/ 1.6 . 1 /libexec/src/net/http/transport.go: 853 + 0x10a6 error: external filter git-lfs smudge %f failed 2 error: external filter git-lfs smudge %f failed fatal: CFHT/D4/cal- 53535 -i-797722_9.fits: smudge filter lfs failed

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Joshua Hoblitt added a comment - 25/Jan/17 5:53 PM

Updating the git-lfs client to 1.5.5 resolved the fault:

mac-os-sierra-build-3:lsstsw square$ rebuild afwdata

             afwdata:  ok (367.5 sec).

          sconsUtils:  ok (1.5 sec).

               scons:  ok (2.2 sec).

              python:  ok (0.9 sec).

             doxygen:  ok (7.0 sec).

# BUILD ID: b2664

             doxygen: 1.8.5.lsst1 ok (20.0 sec).

              python: 0.0.6 ok (2.0 sec).

               scons: 2.5.0.lsst2+1 ok (2.5 sec).

          sconsUtils: 12.1+1 ok (5.0 sec).

             afwdata: 2.2016.10 ..ok (23.4 sec).

# BUILD b2664 completed.

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Joshua Hoblitt added a comment - 25/Jan/17 5:53 PM Updating the git-lfs client to 1.5.5 resolved the fault: mac-os-sierra-build- 3 :lsstsw square$ rebuild afwdata afwdata: ok ( 367.5 sec). sconsUtils: ok ( 1.5 sec). scons: ok ( 2.2 sec). python: ok ( 0.9 sec). doxygen: ok ( 7.0 sec). # BUILD ID: b2664 doxygen: 1.8 . 5 .lsst1 ok ( 20.0 sec). python: 0.0 . 6 ok ( 2.0 sec). scons: 2.5 . 0 .lsst2+ 1 ok ( 2.5 sec). sconsUtils: 12.1 + 1 ok ( 5.0 sec). afwdata: 2.2016 . 10 ..ok ( 23.4 sec). # BUILD b2664 completed.

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Joshua Hoblitt added a comment - 26/Jan/17 3:00 PM

I went ahead and merged a "fix" to lsstsw. Jonathan Sick Could you either (pull from master, rm ${LSSTSW}/lfs/.git-lfs.deployed, and rerun deploy) or start from a new lsstsw clone to verify that this issue is resolved?

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Joshua Hoblitt added a comment - 26/Jan/17 3:00 PM I went ahead and merged a "fix" to lsstsw . Jonathan Sick Could you either (pull from master, rm ${LSSTSW}/lfs/.git-lfs.deployed , and rerun deploy ) or start from a new lsstsw clone to verify that this issue is resolved?

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Jonathan Sick added a comment - 26/Jan/17 10:02 PM

Works! Much thanks Joshua Hoblitt.

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Jonathan Sick added a comment - 26/Jan/17 10:02 PM Works! Much thanks Joshua Hoblitt .

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Joshua Hoblitt added a comment - 27/Jan/17 8:38 AM

Great!

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Joshua Hoblitt added a comment - 27/Jan/17 8:38 AM Great!

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Assignee:: Joshua Hoblitt

Reporter:: Jonathan Sick

Reviewers:: Jonathan Sick

Watchers:: J Matt Peterson [X] (Inactive), Jonathan Sick, Joshua Hoblitt

Votes:: 0 Vote for this issue

Watchers:: 3 Start watching this issue

Dates

Created:: 17/Jan/17 9:45 AM

Updated:: 27/Jan/17 8:38 AM

Resolved:: 27/Jan/17 8:38 AM

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