gopherbot
commented
10 years ago Another error message I get, when trying to run another time:
fatal error: malloc/free - deadlock
[signal 0xb code=0x1 addr=0x0 pc=0x40cec7]
goroutine 928 [running]:
[fp=0x7f84f38f0ae0] runtime.throw(0x5f0120)
/usr/local/go/src/pkg/runtime/panic.c:473 +0x67
[fp=0x7f84f38f0b38] runtime.mallocgc(0x10, 0x100000000, 0x7f8400000001)
/usr/local/go/src/pkg/runtime/zmalloc_linux_amd64.c:33 +0x66
[fp=0x7f84f38f0b58] runtime.mal(0x10)
/usr/local/go/src/pkg/runtime/zmalloc_linux_amd64.c:611 +0x3f
[fp=0x7f84f38f0b90] copyin(0x51dc80, 0x7f84f38f0bd0, 0x7f84f38f0be8)
/usr/local/go/src/pkg/runtime/iface.c:152 +0x5f
[fp=0x7f84f38f0bc8] runtime.convT2E()
/usr/local/go/src/pkg/runtime/iface.c:220 +0x40
[fp=0x7f84f38f0bf8] runtime.newErrorString(0x5ef208, 0x31, 0x7f84f38f0c20)
/usr/local/go/src/pkg/runtime/error.go:74 +0x38
[fp=0x7f84f38f0c38] runtime.panicstring(0x5ef208)
/usr/local/go/src/pkg/runtime/panic.c:486 +0x8b
[fp=0x7f84f38f0c50] runtime.sigpanic()
/usr/local/go/src/pkg/runtime/os_linux.c:236 +0x168
[fp=0x7f84f38f0c90] runtime.MCentral_AllocList(0x7f8504c01c20, 0x20, 0x7f84f38f0cb8)
/usr/local/go/src/pkg/runtime/mcentral.c:63 +0xb7
[fp=0x7f84f38f0cd0] runtime.MCache_Alloc(0x7f84f4bdd788, 0x3, 0x20, 0x1)
/usr/local/go/src/pkg/runtime/mcache.c:24 +0x83
[fp=0x7f84f38f0d28] runtime.mallocgc(0x20, 0x100000001, 0x1)
/usr/local/go/src/pkg/runtime/zmalloc_linux_amd64.c:47 +0xf5
[fp=0x7f84f38f0d68] cnew(0x4fa940, 0x4, 0x1)
/usr/local/go/src/pkg/runtime/zmalloc_linux_amd64.c:655 +0xee
[fp=0x7f84f38f0d88] runtime.cnewarray(0x4fa940, 0x4)
/usr/local/go/src/pkg/runtime/zmalloc_linux_amd64.c:673 +0x38
[fp=0x7f84f38f0da0] makeslice1(0x4f45e0, 0x2, 0x4, 0x7f84f38f0e40)
/usr/local/go/src/pkg/runtime/slice.c:53 +0x45
[fp=0x7f84f38f0dd0] growslice1(0x4f45e0, 0xc201fd1860, 0x2, 0x2, 0x3, ...)
/usr/local/go/src/pkg/runtime/slice.c:212 +0x56
[fp=0x7f84f38f0e18] runtime.growslice(0x4f45e0, 0xc201fd1860, 0x2, 0x2, 0x1, ...)
/usr/local/go/src/pkg/runtime/slice.c:179 +0x9f
[fp=0x7f84f38f0e98] goTree/dataObjects.Sequence.PositionOfMut(0xc21deb6000, 0x123,
0x123, 0x123, 0xc201fd1850, ...)
/data/smew/not-backed-up/forest/cephi/goTree/src/goTree/dataObjects/generation.go:29 +0xa9
[fp=0x7f84f38f0f90] goTree/dataObjects.(*Generation).AddSeq(0xc20dc1cbe0, 0xc21deb6000,
0x123, 0x123, 0x2, ...)
/data/smew/not-backed-up/forest/cephi/goTree/src/goTree/dataObjects/generation.go:122 +0x2c6
----- stack segment boundary ----- 
davecheney
bradfitz
by eau.forest:
My program is quite big, and I can't easily make it reproducible for you. It uses python and go, and I do parallel calculation. It's run perfectly well on osX 10.6 and 10.8, also on Linux Ubuntu 13.10. But I have tried to run it on a server at University, and it does not want to work. It always crash after around 10 min, at different place in my code. But it seems to be usually about making slice. I have try to use different version of go, but it does not work. It seems to run correctly when using only 1 cpu, it's when I try to use multiple cpu that it's crashes. What I don't understand is that it runs correctly on mac and Ubuntu. What do you see instead? panic: invalid memory address or nil pointer dereference fatal error: panic during malloc [signal 0xb code=0x1 addr=0x183 pc=0x4200f6] goroutine 2238 [running]: runtime.throw(0x685eed) /usr/local/go/src/pkg/runtime/panic.c:464 +0x69 fp=0x7f9bd41b8080 runtime.panicstring(0x685c48) /usr/local/go/src/pkg/runtime/panic.c:475 +0x53 fp=0x7f9bd41b80a8 runtime.sigpanic() /usr/local/go/src/pkg/runtime/os_linux.c:234 +0x16a fp=0x7f9bd41b80c0 runtime.mallocgc(0x140, 0x4f91e1, 0x1) /usr/local/go/src/pkg/runtime/malloc.goc:73 +0x116 fp=0x7f9bd41b8130 cnew(0x4f91e0, 0x13a, 0x1) /usr/local/go/src/pkg/runtime/malloc.goc:718 +0xc1 fp=0x7f9bd41b8150 runtime.cnewarray(0x4f91e0, 0x13a) /usr/local/go/src/pkg/runtime/malloc.goc:731 +0x3a fp=0x7f9bd41b8170 makeslice1(0x4f1c20, 0x9d, 0x13a, 0x7f9bd41b8228) /usr/local/go/src/pkg/runtime/slice.c:57 +0x4d fp=0x7f9bd41b8188 growslice1(0x4f1c20, 0xc23a17f1e0, 0x9d, 0x9d, 0xb5, ...) /usr/local/go/src/pkg/runtime/slice.c:113 +0x58 fp=0x7f9bd41b81b8 runtime.growslice(0x4f1c20, 0xc23a17f1e0, 0x9d, 0x9d, 0x18, ...) /usr/local/go/src/pkg/runtime/slice.c:80 +0x9d fp=0x7f9bd41b8200 goTree/big.(*Float).MultiplyFloat64(0xc254c91810, 0x2aebd814d13f2468, 0x0, 0x0, 0x0, ...) /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/big/float.go:450 +0x52c fp=0x7f9bd41b83b8 goTree/estimation.addLikelihoodAfterCoa(0xc22d9cd400, 0x0, 0x2, 0x3) /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/estimation/build1Tree.go:244 +0x2d7 fp=0x7f9bd41b8478 goTree/estimation.makeCoalescence(0xc22d9cd400, 0x0, 0x2, 0x3, 0xc24e55a000, ...) /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/estimation/build1Tree.go:262 +0x4a fp=0x7f9bd41b84a8 goTree/estimation.build1TreeCorrBiasStopEpoch(0xc230f3b1e0, 0x2, 0x2, 0x0, 0xc24b5e6300, ...) /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/estimation/build1Tree.go:755 +0x19bf fp=0x7f9bd41b8748 goTree/estimation.buildSomeTreesCorrBias(0xc23a887000, 0x54, 0x54, 0xa, 0xc2250fdb60, ...) /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/estimation/buildTrees.go:163 +0x1ef fp=0x7f9bd41b8f40 runtime.goexit() /usr/local/go/src/pkg/runtime/proc.c:1394 fp=0x7f9bd41b8f48 created by goTree/estimation.buildTreesCorrBias /data/smew/not-backed-up/forest/cephi/goTree/src/goTree/estimation/buildTrees.go:209 +0x573 Which compiler are you using (5g, 6g, 8g, gccgo)? Not sure Which operating system are you using? Linux 3.10.14-100.fc18.x86_64 Which version are you using? (run 'go version') go1.1.2 Please provide any additional information below.