ETA: Further discussion probably best moved to this thread: Parallel chains not working; different behavior in RStudio and R from Terminal

When running a model with RStan using 4 chains in parallel, I get this error:

```
Error in FUN(X[[i]], ...) :
trying to get slot "mode" from an object of a basic class ("NULL") with no slots
Calls: sampling -> sampling -> .local -> sapply -> lapply -> FUN
```

The same model used to work with RStan and still runs with PyStan just fine.

It looks like this problem has shown up before: R 3.5.1 complains about slot "mode"

However, this time it’s happening with R 3.6.1 and RStan 2.18.2.

Any ideas on fixes or workarounds?

bgoodri
September 17, 2019, 7:43pm
#2
The slot mode thing is a red herring. The sampler returned `NULL`

, which means it aborted. There is usually a message about why if you run it with `chains = 1`

.

1 Like

Huh, now it just aborted almost right away. It used to be that at least a couple chains ran:

```
Chain 1:
Chain 1: Gradient evaluation took 7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.7 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Abort trap: 6
```

ETA: That was when running R at the Terminal. When running from RStudio, it actually works – but only if `chains`

= 1. Otherwise, this is the output:

```
SAMPLING FOR MODEL 'jc' NOW (CHAIN 1).
Chain 1:
Chain 1: Gradient evaluation took 0.00011 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Error in unserialize(socklist[[n]]) : error reading from connection
SAMPLING FOR MODEL 'jc' NOW (CHAIN 2).
Chain 2:
Chain 2: Gradient evaluation took 0.000152 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 1.52 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: Iteration: 1 / 2000 [ 0%] (Warmup)
SAMPLING FOR MODEL 'jc' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 7.9e-05 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.79 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
SAMPLING FOR MODEL 'jc' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.000107 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 1.07 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: Iteration: 1 / 2000 [ 0%] (Warmup)
Chain 2: Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 4: Iteration: 200 / 2000 [ 10%] (Warmup)
Chain 2: Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 4: Iteration: 400 / 2000 [ 20%] (Warmup)
Chain 2: Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 4: Iteration: 600 / 2000 [ 30%] (Warmup)
Chain 2: Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 4: Iteration: 800 / 2000 [ 40%] (Warmup)
Chain 2: Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 2: Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 4: Iteration: 1000 / 2000 [ 50%] (Warmup)
Chain 4: Iteration: 1001 / 2000 [ 50%] (Sampling)
Chain 2: Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 4: Iteration: 1200 / 2000 [ 60%] (Sampling)
Chain 2: Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 4: Iteration: 1400 / 2000 [ 70%] (Sampling)
Chain 2: Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 4: Iteration: 1600 / 2000 [ 80%] (Sampling)
Chain 2: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 4: Iteration: 1800 / 2000 [ 90%] (Sampling)
Chain 4: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 4.21187 seconds (Warm-up)
Chain 4: 3.00345 seconds (Sampling)
Chain 4: 7.21531 seconds (Total)
Chain 4:
Chain 2: Iteration: 2000 / 2000 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 3.86222 seconds (Warm-up)
Chain 2: 3.55775 seconds (Sampling)
Chain 2: 7.41997 seconds (Total)
Chain 2:
Error in serialize(data, node$con, xdr = FALSE) : ignoring SIGPIPE signal
Calls: <Anonymous> ... doTryCatch -> sendData -> sendData.SOCK0node -> serialize
Execution halted
Error in serialize(data, node$con, xdr = FALSE) : ignoring SIGPIPE signal
Calls: <Anonymous> ... doTryCatch -> sendData -> sendData.SOCK0node -> serialize
Execution halted
```

It looks like only chains 2 and 4 actually ran to completion.

bgoodri
September 18, 2019, 5:45pm
#4
Can you post the Stan program?